ISOLATED GLUTAMINASE PROTEIN MUTANTS, METHODS OF USE

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05:46:12
March
05 2016

ISOLATED GLUTAMINASE PROTEIN MUTANTS, METHODS OF USE

United States Patent Application 20160002619

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The present invention relates to a labeled glutaminase (GLS) protein comprising a GLS protein and a fluorescent reporter group attached to the GLS protein, wherein the fluorescent reporter group is attached to the GLS protein within the glutaminase domain pfam04960 of GLS. The present invention also relates to isolated glutaminase protein mutants. Also disclosed is a method of screening for compounds that allosterically bind to a glutaminase protein. The present invention also relates to a method of identifying compounds that inhibit or stabilize tetramer formation of glutaminase protein. The present invention further relates to a screening kit for compounds that inhibit or stabilize tetramer formation.

1. A labeled glutaminase (GLS) protein comprising: a GLS protein and a fluorescent reporter group attached to the GLS protein, wherein the fluorescent reporter group is attached to the GLS protein within the glutaminase domain pfam04960 of GLS.

2. The labeled GLS protein according to claim 1, wherein the GLS protein is a wild type protein.

3. The labeled GLS protein according to claim 1, wherein the GLS protein is a GLS isoform selected from the group consisting of glutaminase C (GAC) and KGA.

4. The labeled GLS protein according to claim 1, wherein the GLS protein is GLS isoform GAC, having an amino acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3.

5. The labeled GLS protein according to claim 1, wherein the GLS protein is GLS isoform KGA, having an amino acid sequence selected from the group consisting of SEQ ID NO:5 and SEQ ID NO:7.

6. The labeled GLS protein according to claim 1, wherein the GLS protein is a mutated GLS protein.

7. The labeled GLS protein according to claim 6, wherein the mutated GLS protein has an amino acid sequence selected from the group consisting of SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12.

8. The labeled GLS protein according to claim 6, wherein the GLS protein is encoded by a nucleic acid molecule corresponding to a nucleotide sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, and SEQ ID NO:8.

9. The labeled GLS protein according to claim 6, wherein the mutated GLS protein is a GLS monomer incapable of forming a GLS dimer.

10. The labeled GLS protein according to claim 1, wherein the fluorescent reporter group is covalently attached to the GLS protein.

11. An isolated glutaminase (GLS) protein or protein fragment comprising a mutated glutaminase domain pfam04960 of SEQ ID NO:19.

12. The isolated GLS protein or protein fragment according to claim 11, wherein the GLS protein or protein fragment is a GLS monomer incapable of forming a GLS dimer.

13. A method of screening for compounds that allosterically bind to a glutaminase (GLS) protein, said method comprising: providing the labeled GLS protein according to claim 1 under conditions effective for the fluorescent reporter group attached to the GLS protein to produce fluorescence at a first level; contacting the labeled GLS protein with one or more candidate compounds; and identifying candidate compounds where said contacting causes the fluorescent reporter group to emit fluorescence at a level above or below the first level as being compounds capable of allosteric binding to the GLS protein.

14. The method according to claim 13, wherein the GLS protein is a monomer.

15. The method according to claim 13, wherein the GLS protein is a dimer.

16. The method according to claim 13 further comprising: contacting the GLS protein, after said identifying, with glutamine under conditions effective to activate the GLS protein; detecting NADH following said contacting the GLS protein, after said identifying, with glutamine; and identifying candidate compounds (1) where NADH is detected as being compounds that do not inhibit GLS protein activity and (2) where NADH is not detected as being compounds that do inhibit GLS protein activity.

17. A method of identifying compounds that inhibit or stabilize tetramer formation of glutaminase (GLS) protein, said method comprising: providing a first labeled GLS dimer protein comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein; providing a second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein, wherein binding of the first labeled GLS protein and the second labeled GLS protein forms a GLS protein tetramer and results in an interaction between the fluorescent donor and the fluorescent acceptor which produces a fluorescence resonance energy transfer at a first level; contacting the first labeled GLS dimer protein and the second labeled GLS dimer protein under conditions effective for the first labeled GLS dimer protein and the second labeled GLS dimer protein to bind and form a GLS protein tetramer; contacting the GLS protein tetramer with a candidate compound; and detecting whether said contacting with the candidate compound alters the fluorescence resonance energy transfer at the first level, wherein detection of the fluorescence resonance energy transfer at the first level indicates that the candidate compound neither inhibits nor stabilizes GLS protein tetramer formation and detection of the fluorescence resonance energy transfer at a level above or below the first level indicates that the candidate compound inhibits or stabilizes tetramer formation of GLS protein.

18. The method according to claim 17, wherein the first and second GLS proteins are wild type proteins.

19. The method according to claim 17, wherein the first and second GLS proteins are GLS isoforms selected from the group consisting of glutaminase C (GAC) and KGA.

20. The method according to claim 17, wherein the first and second GLS proteins are GLS isoform GAC, having an amino acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3.

21. The method according to claim 17, wherein the first and second GLS proteins are GLS isoform KGA, having an amino acid sequence selected from the group consisting of SEQ ID NO:5 and SEQ ID NO:7.

22. The method according to claim 17, wherein the fluorescent donor is covalently attached to the first GLS protein and the fluorescent acceptor is covalently attached to the second GLS protein.

23. The method according to claim 17, wherein the fluorescent donor and fluorescent acceptor are attached to the first and second GLS proteins, respectively, within the glutaminase domain pfam04960 of GLS.

24. A screening kit for compounds that inhibit or stabilize tetramer formation, said kit comprising: a first labeled GLS dimer protein comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein and a second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein, wherein binding of the first labeled GLS protein and the second labeled GLS protein forms a GLS protein tetramer and results in an interaction between the fluorescent donor and the fluorescent acceptor which produces a fluorescence resonance energy transfer.

25. The screening kit according to claim 24, wherein the GLS dimer protein of the first labeled GLS dimer protein and the GLS dimer protein of the second labeled GLS dimer protein are GLS isoform GAC, having an amino acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3.

26. The screening kit according to claim 24, wherein the GLS dimer protein of the first labeled GLS dimer protein and the GLS dimer protein of the second labeled GLS dimer protein are GLS isoform KGA, having an amino acid sequence selected from the group consisting of SEQ ID NO:5 and SEQ ID NO:7.

27. The screening kit according to claim 24, wherein the fluorescent donor and fluorescent acceptor are attached to the GLS dimer protein within the glutaminase domain pfam04960 of GLS.

Description:
This application claims the priority benefit of U.S. Provisional Patent Application Ser. No. 61/770,197, filed Feb. 27, 2013, which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION
The present invention relates to labeled glutaminase proteins, isolated glutaminase protein mutants, methods of screening for compounds that allosterically bind to glutaminase proteins, methods of identifying compounds that inhibit or stabilize tetramer formation of glutaminase proteins, and screening kits for compounds that inhibit or stabilize tetramer formation of glutaminase.

BACKGROUND OF THE INVENTION
Recently, the role of the mitochondrial enzyme glutaminase (“GLS”) has gained significant attention as a therapeutic target for cancer (DeBerardinis et al., “Q's Next: The Diverse Functions of Glutamine in Metabolism, Cell Biology and Cancer,” Oncogene 29:313-324 (2010)). GLS catalyzes the hydrolysis of glutamine to glutamate, which is then used in the TCA cycle of cancer cells undergoing an aberrant glycolytic flux (i.e., the “Warburg effect”) as a non-glucose derived source for anaplerosis. The elevation in glutamine metabolism exhibited by cancer cells (“glutamine addiction”) is thought to be critical for sustaining their proliferative capacity as well as for other aspects of their transformed phenotypes (Wise et al., “Glutamine Addiction: A New Therapeutic Target in Cancer,” Trends Biochem. Sci. 35(8):427-433 (2010); Vander Heiden et al., “Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation,” Science 324:1029-1033 (2009); Wang et al., “Targeting Mitochondrial Glutaminase Activity Inhibits Oncogenic Transformation,” Cancer Cell 18:207-219 (2010); Gao et al., “c-Myc Suppression of miR-23a/b Enhances Mitochondrial Glutaminase Expression and Glutamine Metabolism,” Nature 458:762-76r (2009); Ward et al., “Metabolic Reprogramming: A Cancer Hallmark Even Warburg Did Not Anticipate,” Cancer Cell 21:297-309 (2012)). Work from the inventors' laboratory has shown that a specific GLS splice variant, called GAC, plays an essential role in the transformation of fibroblasts by oncogenic Dbl (for Diffuse B Cell lymphoma), a guanine nucleotide exchange factor (GEF) that activates the small GTPases Cdc42, Rac, and Rho (Wang et al., “Targeting Mitochondrial Glutaminase Activity Inhibits Oncogenic Transformation,” Cancer Cell 18:207-219 (2010); Lin et al., “Specific Contributions of the Small GTPases Rho, Rac, and cdc42 to Dbl Transformation,” J. Biol. Chem. 274:23633-23641 (1999)). Likewise, it has been found that the growth of fibroblasts transformed by oncogenic Rho GTPase mutants, as well as the proliferative and invasive activities of a variety of cancer cells, are dependent upon GAC activity (Katt et al., “Dibenzophenanthridinones as Inhibitors of Glutaminase C and Cancer Cell Proliferation,” Mol. Cancer Ther. 11:1269-1278 (2012)). Thus, given the importance of GAC expression and activation for oncogenic transformation, the identification of small molecule inhibitors that target this metabolic enzyme offers new opportunities for the development of anti-cancer drugs.

A commonly used active site-directed inhibitor of members of the glutaminase family is DON (for Diazo-O-norleucine), a glutamine derivative that forms a stable acyl-enzyme intermediate with the catalytic serine residue responsible for deamidase activity. Because DON reacts with the highly conserved glutaminase active site which is present in all members of the β-lactamase superfamily (Thangavelu et al., “Structural Basis for the Active Site Inhibition Mechanism of Human Kidney-Type Glutaminase (KGA),” Scientific Reports 4:3827 (1-7) (2014); Shelton et al., “Glutamine Targeting Inhibits Systemic Metastasis in the VM-M3 Murine Tumor Model,” Int. J. Cancer 127(10):2478-2485 (2010)), it has been shown to have severe off-target effects and, therefore, does not represent an ideal candidate for selectively inhibiting the elevated glutamine metabolism characteristic of cancer cells (Rahman et al., “Phase I Study and Clinical Pharmacology of 6-diazo-5-oxo-L-norleucine (DON),” Investigational New Drugs 3:369-374 (1985)). However, two classes of allosteric inhibitors of GAC have been identified which offer more promising options as lead compounds for the development of cancer therapeutics. One of these is BPTES (bis-2-(5-phenylacetamido-1,2,4-thiadiazol-2-yl)ethyl sulfide), a reversible inhibitor of GAC which has been extensively characterized both biochemically and through steady state kinetic analyses. High-resolution x-ray structures of the GAC-BPTES complex show that BPTES effectively traps GAC as an inactive tetramer (DeLaBarre et al., “Full-Length Human Glutaminase in Complex with an Allosteric Inhibitor,” Biochemistry 50:10764-10770 (2011); Thangavelu et al., “Structural Basis for the Allosteric Inhibitory Mechanism of Human Kidney-Type Glutaminase (KGA) and its Regulation by Raf-Mek-Erk Signaling in Cancer Cell Metabolism,” Proc. Natl. Acad. Sci. 109(20):7705-7710 (2012); Cassago et al., “Mitochondrial Localization and Structure-Based Phosphate Activation Mechanism of Glutaminase C with Implications for Cancer Metabolism,” Proc. Natl. Acad. Sci. 109(4):1092-1097 (2012)).

A more recently identified class of allosteric inhibitors of GAC which offer the advantage of being highly specific in their ability to inhibit the growth and invasive activity of cancer cells, while having little effect on normal (non-transformed) cells, is represented by the benzophenanthridinone, designated as 968 (Wang et al., “Targeting Mitochondrial Glutaminase Activity Inhibits Oncogenic Transformation,” Cancer Cell 18:207-219 (2010); Katt et al., “Dibenzophenanthridinones as Inhibitors of Glutaminase C and Cancer Cell Proliferation,” Mol. Cancer Ther. 11:1269-1278 (2012)). The specificity exhibited by 968 for inhibiting the transformed features of cancer cells holds exciting promise for selectively attacking those metabolic changes critical for malignant transformation. However, thus far very little is known regarding how 968 binds to GAC and the mechanisms by which it blocks GAC activation.

The present invention is directed to overcoming these and other deficiencies in the art.

SUMMARY OF THE INVENTION
One aspect of the present invention relates to a labeled glutaminase (GLS) protein comprising a GLS protein and a fluorescent reporter group attached to the GLS protein, where the fluorescent reporter group is attached to the GLS protein within the glutaminase domain pfam04960 of GLS.

Another aspect of the present invention relates to an isolated glutaminase (GLS) protein or protein fragment comprising a mutated glutaminase domain pfam04960 of SEQ ID NO:19.

A further aspect of the present invention relates to a method of screening for compounds that allosterically bind to a glutaminase (GLS) protein. This method involves providing the labeled GLS protein of the present invention under conditions effective for the fluorescent reporter group attached to the GLS protein to produce fluorescence at a first level. The labeled GLS protein is contacted with one or more candidate compounds. Candidate compounds where said contacting causes the fluorescent reporter group to emit fluorescence at a level above or below the first level are identified as being compounds capable of allosteric binding to the GLS protein.

Yet another aspect of the present invention relates to a method of identifying compounds that inhibit or stabilize tetramer formation of glutaminase (GLS) protein. This method involves providing a first labeled GLS dimer protein comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein. A second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein is also provided, where binding of the first labeled GLS protein and the second labeled GLS protein forms a GLS protein tetramer and results in an interaction between the fluorescent donor and the fluorescent acceptor which produces a fluorescence resonance energy transfer at a first level. The first labeled GLS dimer protein and the second labeled GLS dimer protein are contacted under conditions effective for the first labeled GLS dimer protein and the second labeled GLS dimer protein to bind and form a GLS protein tetramer. The GLS protein tetramer is contacted with a candidate compound. The method further involves detecting whether said contacting with the candidate compound alters the fluorescence resonance energy transfer at the first level. Detection of the fluorescence resonance energy transfer at the first level indicates that the candidate compound neither inhibits nor stabilizes GLS protein tetramer formation and detection of the fluorescence resonance energy transfer at a level above or below the first level indicates that the candidate compound inhibits or stabilizes tetramer formation of GLS protein.

Yet a further aspect of the present invention relates to a screening kit for compounds that inhibit or stabilize tetramer formation. The kit includes a first labeled GLS dimer protein comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein. Also included in the kit is a second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein. Binding of the first labeled GLS protein and the second labeled GLS protein forms a GLS protein tetramer and results in an interaction between the fluorescent donor and the fluorescent acceptor which produces a fluorescence resonance energy transfer.

In the present invention, the binding of 968 to a mutant form of a GLS protein splice variant that is trapped in the monomeric state is characterized, and it is shown that this binding correlates with inhibition of recombinant GLS in a real-time coupled binding and activity assay. Novel fluorescence read-outs are used that, for the first time, allow definitive demonstration that 968 and related compounds directly bind to GLS. Moreover, it is shown that the binding of 968 to the GLS splice variant correlates well with its inhibition of the protein's activity, and importantly, with its ability to block the growth of transformed cells. These findings permit the development of an important new class of cancer therapeutics.

BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-F illustrate the development of a fluorescence assay to monitor subunit interactions. FIG. 1A is a schematic model of a FRET assay developed to detect dynamic tetramer formation. FIG. 1B illustrates the kinetics of labeling wild type (“WT”) GAC with ALEXA FLUOR® 488 succinimidyl ester analyzed by SDS-PAGE and visualized under UV illumination. 488-labeled GAC was analyzed using analytical gel filtration to illustrate the purification of a covalently modified GAC along with eluting at the same volume as an equivalent concentration of unlabeled WT-GAC. FIG. 1C shows that 25 nM 488-WT-GAC fluorescence is quenched upon addition of QSY® 9-WT-GAC (acceptor) in a dose dependent manner (quantified in FIG. 1D), and can be rescued by addition of a 10-fold excess unlabeled WT-GAC. In FIG. 1D, FRET values from FIG. 1C (left axis) were overlaid with concentration dependent activation (in absence of Pi) of WT-GAC (right axis) in the presence of 20 mM glutamine measured in an independent two-step activity assay. As illustrated in FIG. 1E, QSY® 9-GAC-488-GAC tetramers were equilibrated by adding 100 nM QSY® 9-WT-GAC to 25 nM 488-WT-GAC, and the effects of phosphate addition on FRET was followed by addition of various phosphate concentrations at 630 seconds. In FIG. 1F, FRET values that resulted from injection of phosphate from FIG. 1E (left axis) were overlaid with phosphate activation of 50 nM WT-GAC in the presence of 20 mM glutamine (right axis) measured in an independent two-step activity assay.

FIGS. 2A-B illustrate that mutating specific residues at the GAC monomer and dimer interface traps mutants in a defined oligomeric state. FIG. 2A is the crystal structure of the tetramer form of GAC (PDB 3SS3), highlighting critical contacts for monomer-monomer contact (top) and dimer-dimer contact (bottom). Interfaces are presented as B-factor representations and not cartoons to facilitate visualization of the interactions. FIG. 2B is an overlay of Superdex200 preparative chromatograms of purified mutants.

FIGS. 3A-C illustrate that WT GAC accesses monomer, dimer, and larger oligomeric species in a concentration and phosphate dependent manner. FIG. 3A is a graph of analytical gel filtration profiles of WT GAC from a 250 μL injection of either 5 mg/mL or 0.5 mg/mL samples in the presence or absence of 50 mM K2HPO4 in the gel filtration buffer showing a strong correlation of oligomeric state with GAC concentration and inorganic phosphate, whereas the same conditions of the D391K-GAC (FIG. 3B) or K316E-D391K-R459E-GAC (FIG. 3C) does not affect oligomerization. Notably, D391K-GAC (FIG. 3B) was found to have two populations when 0.5 mg/mL samples were injected but not 5 mg/mL, characteristic of a monomer and dimer population that is concentration dependent.

FIGS. 4A-F define the oligomeric species of GAC mutants. In particular, multi-angle light scattering profiles of WT-GAC (FIG. 4A), D391K-GAC (FIG. 4B), K316E-D391K-R459E-GAC (FIG. 4C), and K316E-GAC (FIG. 4D) were obtained following SEC and subsequent MALS analysis, where elution of each species was monitored using refractive index (left axis). Upon elution, light scattering data was collected and then used to calculate the molecular weight and polydispersity for the species eluted (right axis). Reference lines for the molecular weights of the monomer, dimer, and tetramer forms of GAC are included at 58 kD, 116 kD, and 230 kD respectively. In FIG. 4E, 200 nM of QSY® 9-WT-GAC, QSY® 9-D391K-GAC, or QSY® 9-K316E-D391K-R459E was added to 20 nM of 488-WT-GAC. In FIG. 4F, WT GAC and GAC mutants were titrated and added to an assay of 20 mM glutamine in the absence of phosphate to show no concentration dependent activation was observed of purified GAC mutants.

FIGS. 5A-C illustrate that the effects of allosteric inhibitors BPTES and 968 on tetramer formation leads to direct binding read out of 968 and 488-GAC. FIG. 5A is a graph showing that addition of 10 μM BPTES to an equilibrated sample of 20 nM 488-GAC and 200 nM QSY® 9-GAC induces tetramer formation that is not reversible by addition of a 10-fold excess of unlabeled GAC, whereas addition of 25 μM of 968 induces a marked quench in 488-GAC fluorescence with partial recovery by the addition of a 10-fold excess of unlabeled GAC. In FIG. 5B, fluorescence quenching upon addition of 968 to 10 nM 488-GAC in the absence of QSY® 9-GAC shows a concentration dependent quenching interaction. FIG. 5C is an overlay of 968 inhibition of 10 nM WT-GAC activity and 968 quenching of 10 nM 488-GAC fluorescence.

FIGS. 6A-F illustrate coupling real time drug binding with enzymatic activity. FIG. 6A is a schematic model of a real time drug binding assay coupled to a real-time activity assay. Binding is first monitored by observing 488-GAC fluorescence, followed by observation of NADH fluorescence that is produced upon the addition of the substrate for GAC, glutamine, and the activator inorganic phosphate, in the presence of 10 Units/mL glutamate dehydrogenase (GDH) and 2 mM NAD+. In the graph of FIG. 6B, 10 nM 488-GAC (520 nm emission) was monitored upon addition of 968, BPTES, or DMSO at 30 seconds, and NADH fluorescence (460 nm emission) was monitored following the addition of 20 mM glutamine and 50 mM phosphate at 120 seconds. FIGS. 6C-D illustrate the results of a coupled real time binding and activity assay of 10 nM 488-GAC and 10 nM WT-GAC using 968 and a less potent 968-analogue, WPK968. FIGS. 6E-F illustrate the results of a coupled real time binding and activity assay of 10 nM 488-GAC with 968-analogues 031 and 742, previously reported as GAC inhibitors.

FIGS. 7A-B illustrate that the small molecule 968 preferentially binds to GAC monomer. FIG. 7A is a plot illustrating 488 fluorescence quenching of 20 nM 488-labeled WT GAC, dimer, and monomer GAC mutants upon 968 titration. FIG. 7B shows in vitro inhibition curves of 50 nM (closed circles) and 5 nM WT-GAC (open circles) with increasing concentrations of pre-incubated 968, where primary GAC species at each concentration is a dimer/tetramer or monomer/dimer, respectively. Overlaid is the dose dependent 968 inhibition of the ability of Dbl-transformed MEFs to form foci (triangles), adapted from Wang et al., “Targeting Mitochondrial Glutaminase Activity Inhibits Oncogenic Transformation,” Cancer Cell 18:207-219 (2010), which is hereby incorporated by reference in its entirety.

FIGS. 8A-C illustrate the identification of a small molecule probe labeling site. In FIG. 8A, 0.6 mg/mL 488 labeled KGA and GAC samples were incubated with 25 μg/mL porcine trypsin (Sigma) on ice for 15 minutes or 60 minutes, at which point Soy Bean Trypsin Inhibitor (SBTI, Sigma) was added to make 20 μg/mL. Loading buffer was added and samples were heated at 95° C. for 2 min and ran on a precast 4-12% Tris-Glycine gel (Invitrogen) for SDS PAGE. The gel was visualized under UV illumination and then transferred to a PVDF membrane to be developed following Western immunoblot with rabbit HRP conjugated anti-GAC antibody raised against the C-terminal GAC peptide (SEQ ID NO:3) highlighted in FIG. 8C. The anti-GAC antibody recognition sequence (SEQ ID NO:13) is set forth in bold in FIG. 8C. In FIG. 8B, the same protocol was followed as in FIG. 8A, where 2.85 mg/mL 488 labeled GAC was incubated with 16.7 μg/mL porcine trypsin on ice for 15 minutes (left of standards) or 30 minutes (right of standards) after which 50 μg/mL SBTI was added. Samples were separated on a 4-12% Tris-Glycine gel following SDS PAGE, and samples for sequencing were cut from adjacent lanes before transfer to a PVDF membrane under UV illumination to identify the peptide fragment of approximately 25 kD. Samples were submitted to Cornell University Mass Spectrometry Core facility, and the resulting identified peptides are underlined in FIG. 8C, resulting in identification of site of modification to be within the glutaminase domain.

FIGS. 9A-B illustrate that the alternate splice variant KGA behaves like GAC in a FRET assay. In FIG. 9A, 10 nM 488-KGA was equilibrated in 50 mM Tris-Acetate (pH=8.5) 0.1 mM EDTA at 20° C. for 2 minutes before adding 40 μL of the appropriate concentration of QSY® 9-KGA and allowed to equilibrate for 5 minutes while monitoring 488-KGA fluorescence. After 5 minutes, the appropriate volume of 33.25 μM (for concentrations up to 200 nM labeled protein) or 69.5 μM (for concentrations above 200 nM labeled protein) unlabeled WT-KGA was added to make the final concentration of unlabeled KGA to be ten-times the concentration of labeled KGA. The FRET values at 5 minutes were quantified and displayed in FIG. 9B versus total labeled protein concentration and combined with FRET measurements from 488-GAC and QSY® 9-GAC titration.

FIGS. 10A-B illustrate measuring of the monomer-monomer binding affinity. In FIG. 10A, 5 nM 488-D391K-GAC was equilibrated in 50 mM Tris-Acetate (pH=8.5) 0.1 mM EDTA at 20° C. for 2 minutes before the experiment was started. An appropriate volume of 4.4 μM QSY® 9-D391K-GAC was added to 5 nM 488-D391K-GAC and 520 nm emission was monitored for 10 minutes. In FIG. 10B, FRET values from FIG. 10A were plotted in a sigma plot and fit to non-linear regression simple ligand binding equation (line).

FIG. 11 is a sequence alignment of four mutated GLS proteins according to one aspect of the present invention, including human GAC (SEQ ID NO:12), mouse GAC (SEQ ID NO:11), human KGA (SEQ ID NO:10), and mouse KGA (SEQ ID NO:9).

DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to labeled glutaminase proteins and isolated glutaminase protein mutants. In addition, the present invention relates to methods of using these proteins in a method for screening for compounds that allosterically bind to a glutaminase protein and a method of identifying compounds that inhibit or stabilize tetramer formation of a glutaminase protein. The present invention further relates to a screening kit for compounds that inhibit or stabilize tetramer formation.

According to a first aspect, the present invention relates to a labeled glutaminase (GLS) protein comprising a GLS protein and a fluorescent reporter group attached to the GLS protein, where the fluorescent reporter group is attached to the GLS protein within the glutaminase domain pfam04960 of GLS.

According to this aspect of the present invention, glutaminase proteins include wild type proteins, including, for example, GLS isoforms GAC and KGA from human and mouse. The GLS isoforms GAC and KGA are splice variants of each other. Specifically, their C-terminal regions are unique (i.e., residues 550-603 of mouse GAC and residues 550-674 of mouse KGA). Likewise, human GAC and KGA proteins each have unique C-terminal regions (i.e., residues 545-598 of human GAC and residues 545-669 of human KGA). In each of the mouse and human GAC and KGA proteins, amino acid residues 1-72 comprise the mitochondrial targeting sequence.

A further aspect of the present invention relates to a method of screening for compounds that allosterically bind to a glutaminase (GLS) protein. This method involves providing the labeled GLS protein of the present invention under conditions effective for the fluorescent reporter group attached to the GLS protein to produce fluorescence at a first level. The labeled GLS protein is contacted with a candidate compound. Candidate compounds where said contacting causes the fluorescent reporter group to emit fluorescence at a level above or below the first level are identified as being compounds capable of allosteric binding to the GLS protein.

In carrying out this and other aspects of the present invention, providing the labeled GLS protein can be accomplished as described supra. In addition, the GLS protein used in this and other aspects of the present invention is as described supra.

This method of the present invention may be carried out in a cell, but is not necessarily carried out in a cell. When carried out in a cell, the GLS protein may be recombinantly expressed, as described supra, and the fluorescent reporter is attached to the GLS protein as described supra to provide the labeled GLS protein.

The labeled GLS protein, by its fluorescent label, emits fluorescence at first level (e.g., a particular wavelength or intensity associated with the fluorescent reporter group). A candidate compound is a compound that causes the fluorescent reporter group to emit a fluorescence at a level above or below the first level, or causes a detectable change in fluorescence (e.g., a shift in the fluorescence wavelength or intensity, or a change in fluorescence lifetime) of the fluorescent reporter group. Detecting a change in fluorescence in this and other aspects of the present invention may be carried out by visual observation. Alternatively, detecting a change in fluorescence may be carried out with a spectrophotometer, or a microscope or macroscope system coupled to a camera or photomultiplier tube. Coupled with proper instrumentation, the optical readout can be followed in real time to obtain spatio-temporal information (functional intracellular imaging).

According to this aspect of the present invention, the GLS protein is, according to one embodiment, a monomer. According to an alternative embodiment, the GLS protein is a dimer.

One embodiment of this method of the present invention is illustrated in FIG. 6A. On the left side of the schematic illustration of FIG. 6A, a GLS protein dimer is shown to be labeled with ALEXA FLUOR® 488 succinimidyl ester (“488-GAC”). This GLS protein dimer emits a high fluorescence. When contacted with candidate compound 968, 488-GAC emits a low fluorescence. In other words, candidate compound 968 binds the GLS protein and causes the fluorescent reporter group ALEXA FLUOR® 488 attached to the GLS protein to emit a fluorescence at a level below the first level (i.e., the level of fluorescence emitted by 488-GAC in the absence of contact with candidate compound 968).

The method according to this aspect of the present invention may further involve contacting the GLS protein, after identifying candidate compounds, with glutamine under conditions effective to activate the GLS protein. NADH is detected following the contacting with the GLS protein, after said identifying with glutamine. Candidate compounds (1) where NADH is detected are identified as being compounds that do not inhibit GLS protein activity and (2) where NADH is not detected are identified as being compounds that do inhibit GLS protein activity. This embodiment is also illustrated in FIG. 6A, where 488-GAC:968, i.e., the labeled GLS protein bound by a candidate compound is contacted with glutamine (Gln+Pi) under conditions to activate the GLS protein to form a GLS protein tetramer (illustrated in the right side of the schematic in FIG. 6A). The tetramer form of the GLS protein catalyzes the reaction of glutamine to NADH, as illustrated in FIG. 6A. Thus, the detection of NADH in carrying out this method of the present invention is indicative of the candidate compound not inhibiting GLS protein activity (despite binding GLS protein). Where NADH is not detected, the candidate compound is identified as a GLS protein activity inhibitor.

Yet another aspect of the present invention relates to a method of identifying compounds that inhibit or stabilize tetramer formation of glutaminase (GLS) protein. This method involves providing a first labeled GLS dimer protein comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein. A second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein is also provided, where binding of the first labeled GLS protein and the second labeled GLS protein forms a GLS protein tetramer and results in an interaction between the fluorescent donor and the fluorescent acceptor which produces a fluorescence resonance energy transfer at a first level. The first labeled GLS dimer protein and the second labeled GLS dimer protein are contacted under conditions effective for the first labeled GLS dimer protein and the second labeled GLS dimer protein to bind and form a GLS protein tetramer. The GLS protein tetramer is contacted with a candidate compound. The method further involves detecting whether said contacting with the candidate compound alters the fluorescence resonance energy transfer at the first level. Detection of the fluorescence resonance energy transfer at the first level indicates that the candidate compound neither inhibits nor stabilizes GLS protein tetramer formation and detection of the fluorescence resonance energy transfer at a level above or below the first level indicates that the candidate compound inhibits or stabilizes tetramer formation of GLS protein.

According to the method of this aspect of the present invention, the first and second GLS proteins are wild type proteins. According to one embodiment, the first and second proteins are GLS isoforms selected from GAC and KGA. Preferably, the first and second proteins are a single GLS isoform, e.g., the first and second proteins are both GAC or the first and second proteins are both KGA.

In carrying out this method of the present invention, the GLS dimer proteins may be labeled with labels discussed supra. However, in carrying out this method, the labels are capable of forming FRET pairs, where fluorescence energy from a fluorescent donor probe can be transferred to an absorbant but not necessarily fluorescent accepter probe (e.g., non-fluorescent QSY dyes available from MOLECULAR PROBES® (Thermo Fisher Scientific, Inc.)). Any FRET pair is suitable for this method of the present invention involving the readout of inhibition or stabilization of GLS protein tetramer formation. In one specific embodiment, the fluorescent donor is ALEXA FLUOR® 488 succinimidyl ester and the fluorescent acceptor is QSY® 9 succinimidyl ester, both of which are MOLECULAR PROBES® obtainable from Thermo Fisher Scientific, Inc. Other donors and acceptors are well known and can also be used.

One embodiment of this method of the present invention is illustrated in the schematic diagram of FIG. 1A. As illustrated on the left side of the schematic in FIG. 1A, a first labeled GLS dimer protein is provided comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein. Specifically, the GLS dimer protein is isoform GAC labeled with ALEXA FLUOR® 488 succinimidyl ester (“488-GAC”). This first labeled GLS dimer protein is a high fluorescence donor protein. A second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein is also provided, as illustrated in FIG. 1A by the dimer labeled “QSY9-GAC.” Specifically, this dimer protein is the GLS isoform GAC labeled with the fluorescence acceptor QSY® 9 succinimidyl ester. As illustrated on the right side of the schematic of FIG. 1A, binding of the first labeled GLS protein (i.e., 488-GAC) and the second labeled GLS protein (i.e., QSY9-GAC) forms a GLS protein tetramer and results in an interaction between the fluorescent donor (ALEXA FLUOR® 488 succinimidyl ester) and the fluorescence acceptor (QSY® 9 succinimidyl ester) to produce a fluorescence resonance energy transfer at a first level (“FRET” in FIG. 1A). This FRET scenario is then used to identify compounds that inhibit or stabilize tetramer formation of glutaminase (GLS) protein according to the method of this aspect of the present invention.

Specifically, the first labeled GLS dimer protein (i.e., 488-GAC) and the second labeled GLS dimer protein (i.e., QSY9-GAC) are contacted (e.g., brought into contact with each other) under conditions effective for the first labeled GLS dimer protein and the second labeled GLS dimer protein to bind and form a GLS protein tetramer, as illustrated in FIG. 1A. The GLS protein tetramer may then be contacted with a candidate compound. The method further involves detecting whether said contacting with the candidate compound alters the fluorescence resonance energy transfer at the first level. In other words, in the absence of a candidate compound, the FRET pair experiences a fluorescence resonance energy transfer at a particular level determined by the donor and acceptor. If, after coming into contact with a candidate compound, the fluorescence resonance energy transfer is unaltered, the candidate compound is determined to neither inhibit nor stabilize GLS protein tetramer formation. If, on the other hand, the fluorescence resonance energy transfer is altered (e.g., is above or below the fluorescence resonance energy transfer of the tetramer in the absence of the candidate compound), then the candidate compound is determined to inhibit or stabilize tetramer formation of GLS protein.

In one embodiment, this method of the present invention is carried out with a population of dimer proteins comprising donors and a population of dimer proteins comprising acceptors. Under certain conditions, about one-half of the dimers will form tetramers to produce a fluorescence resonance energy transfer (e.g., will establish an equilibrium of dimers:tetramers). In carrying out the method according to this aspect of the present invention, the population of dimers:tetramers is contacted with a candidate compound. A candidate compound capable of stabilizing tetramer formation of GLS protein will cause a shift in the equilibrium of dimers:tetramers to increase the number of tetramers formed and, thereby, alter the detectable level of fluorescence energy transfer. Alternatively, a candidate compound capable of inhibiting tetramer formation of GLS protein will cause a shift in the equilibrium of dimers:tetramers in the opposite direction to decrease the number of tetramers formed and, thereby, alter the detectable level of fluorescence energy transfer.

This phenomenon is illustrated in FIG. 5A, in the line representing (+) 10 μM BPTES. Specifically, beginning at the left of the graph, a GLS dimer protein labeled with a donor group emits a fluorescence that is quenched upon coming into contact with a GLS dimer protein labeled with an acceptor group (“Acceptor”). This quenching in fluorescence upon contact between the donor and acceptor occurs as the fluorescence of the donor is absorbed by the acceptor. Upon contact with a candidate compound (“968/BPTES”), further quenching is detected, because 968 and BPTES are compounds that stabilize tetramer formation. In other words, contact of the FRET pair of GLS dimers by a compound that stabilizes tetramer formation caused additional formation of FRET pairs and, as a result, further absorbance by the acceptor from the donor.

Yet a further aspect of the present invention relates to a screening kit for compounds that inhibit or stabilize tetramer formation. The kit includes a first labeled GLS dimer protein comprising a GLS protein and a fluorescent donor attached to the GLS dimer protein. Also included in the kit is a second labeled GLS dimer protein comprising a GLS protein and a fluorescent acceptor attached to the GLS protein. Binding of the first labeled GLS protein and the second labeled GLS protein forms a GLS protein tetramer and results in an interaction between the fluorescent donor and the fluorescent acceptor which produces a fluorescence resonance energy transfer.

EXAMPLES
The following examples are provided to illustrate embodiments of the present invention but are by no means intended to limit its scope.

Example 1
Development of Fluorescently Labeled Recombinant GAC, Small Molecule Probes for Use in FRET Assays, and Direct Binding Readouts for Allosteric Inhibitors of GAC
Materials and Methods

Recombinant Glutaminase Preparation and Labeling with Small Molecule Probes

A mouse kidney type glutaminase isoform 1 (KGA, NP 001074550.1 , which is hereby incorporated by reference in its entirety (SEQ ID NO: 7)) and isoform 2 (GAC, NP 001106854.1 , which is hereby incorporated by reference in its entirety (SEQ ID NO:3)) plasmid (residues 72-603 for GAC, 72-674 for KGA) was cloned into a pET23a vector containing an N-terminal histidine (His)-tag and thrombin cleavage site.

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