# Patent

## Title
Pharmaceutical compositions and methods for treating cancer and biomarkers for drug screening

## Abstract

A pharmaceutical composition comprising sorafenib and GW5074. Said combination therapy inhibits cancer cell growth via c-Raf-PP2A-DAPK signaling transduction pathway in either in vitro or in preclinical animal model for orthotopic spontaneous kidney cancer which simulates clinical symptoms. Formation of the bond between c-Raf and GW5074 leads to conformational change which consequently increases the affinity between sorafenib and c-Raf. Binding with the specific drug target facilitates serine 308 dephosphorylation of DAPK by PP2A and induces necrosis in cancer cells. Serine 308 of DAPK protein may also be used as a biomarker for drug screening. This study provides a novel pharmaceutical composition comprising sorafenib and GW5074, a protein complex target consisting of c-Raf and DAPK for drug designing, as well as biomarkers including c-Raf protein, DAPK protein and phosphorylation status of DAPK for drug screening.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a division of application Ser. No. 13/903,504, filed on May 28, 2013, and now for which the benefit is claimed under 35 U.S.C §121; the content of each of the above-mentioned patent application is hereby incorporated by reference herein in its entirety and made a part of this specification.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a pharmaceutical composition for treating cancer, comprising sorafenib and GW5074. The invention also discloses a method for dissociating a protein complex consisting of c-Raf and DAPK by drugs, which can then be used as targets for designing new drugs. Additionally, the invention further provides a method for screening drugs utilizing proteins c-Raf and DAPK as well as the phosphorylation status of DAPK.
2. Description of the Prior Art
Activation of the proto-oncogenes or deficiency of the tumor suppressor genes often leads to cancer cell development. Ras is a proto-oncogene and activation of Ras protein is normally triggered by receptor tyrosine kinase (TKIs) on the cell membrane. Activated Ras protein binds with RAF and subsequently transmits the signal downstream to activate the MAPK pathway which, in turn, regulates cell growth as well as cell differentiation. Activated Grb-sos protein arising from binding of a growth factor to its receptor on the cell membrane leads to phosphorylation of downstream Ras-GDP protein, and the resulting Ras-GTP then binds to the N-terminus of Raf protein and activates Raf, which further regulates the activation of ERK through phosphorylation of MEK. Next, activated ERK enters the cell nucleus and induces cancer cell proliferation. Therefore, countless drugs that are designed specifically against these proto-oncogenes such as these tyrosine kinase inhibitors (TKIs) were generated, only to discover that many cancer patients developed drug resistance during the treatment. Consequently, combination therapy that specifically targets the signaling transduction pathway of tyrosine kinase has become a common treatment method.
Angiogenesis as well as cell proliferation play essential roles in tumor growth. Binding of vascular endothelial growth factor (VEGF-A) released from cancer cells in vast amounts to vascular endothelial growth factor receptor (VEGFR-2) on the surface of the endothelial cells of a tumor activates the signaling transduction pathway of Raf/mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) which in turn induces angiogenesis of endothelial cells. Meanwhile, the Ras-ERK pathway also facilitates cancer cell proliferation. In addition, loss of regulation of the Ras-Raf-ERK pathway has been shown in a number of tumor cell lines. Thus, VEGF and Raf may be the best targets for inhibition of tumor growth.
Sorafenib (Nexavar®, BAY 43-9006, Bayer HealthCare Pharmaceuticals) is an oral Multi-Kinase Inhibitor commonly used for treating various cancers. Sorafenib can inhibit proteins such as Raf, VEGF receptor, platelet-derived growth factor (PDGF) receptor, KIT and Fms-like tyrosine kinase-3 (FLT-3). A number of studies have indicated that sorafenib inhibits tumor growth by inhibiting Raf signaling pathway in different cancer cells while suppressing proliferation of the endothelia cells surrounding cancer cells through inhibition of VEGF as well as PDGF signaling pathways, and subsequently induces cancer cell death. The design and test results of these drugs are ideal. However, after few years of clinical applications, it was unfortunate discovered that, although the tumor size at the early stage of treatment was efficiently inhibited by sorafenib, the drug not only cannot eradicate the tumor completely, but causes serious side effects. Moreover, these treated cancer cells developed drug resistance after prolonged treatment. Additionally, in recent years, certain studies have shown that inhibition of Raf signaling pathway in cancer cells leads to reduced inhibition of sorafenib due to alternative regulation by different molecules in cancer cells. Most importantly, some evidence further indicated that the inhibition effects of sorafenib on cancer cells may not be regulated by the Raf pathway. Hence, the aforementioned imperfections need to be further improved.
SUMMARY OF THE INVENTION
Treating cancer patients with sorafenib at an early stage can indeed efficiently inhibit tumor size. Nonetheless, this treatment cannot eliminate tumors completely. Even worse, severe side effects usually appear after prolonged treatment and tumor cells may consequently develop drug resistance. This indicates that the current treatment is not an effective method and further improvements are urgently required. Therefore, the present invention reveals certain discoveries, comprising: (1) a novel combination therapy of sorafenib and GW5074; (2) a target for new drug design to effectively kill cells by triggering cell necroptosis induced by dissociation of c-Raf and DAPK; and (3) a biomarker used for drug screening utilizing proteins c-Raf and DAPK as well as the phosphorylation status of DAPK.
In one aspect, the present invention provides a pharmaceutical composition for treating cancer, comprising sorafenib and GW5074 (3-(3,5-Dibromo-4-hydroxy-benzylidene)-5-iodo-1,3-dihydro-indol-2-one).
According to the invention, the composition is administered separately, concurrently, or orderly.
According to the invention, the cancer comprises renal cell carcinoma, prostate cancer, breast cancer, lung cancer, cervical carcinoma, oral cancer, glioma, urothelial cell carcinoma, or melanoma.
According to the invention, the pharmaceutical composition further includes pharmaceutically acceptable salts or vehicles. The aforementioned vehicles comprise excipients, diluents, thickeners, fillers, binders, disintegrants, lubricants, oil or non-oil agents, surfactants, suspending agents, gelling agents, adjuvants, preservatives, antioxidants, stabilizers, coloring agents or spices thereof.
According to the invention, the pharmaceutical composition is for oral administration, immersion, injection, topical application or patch administration.
According to the pharmaceutical composition of the invention, GW5074 binds to c-Raf protein (SEQ ID NO: 1) and induces conformational change of c-Raf, which consequently increases the binding affinity of sorafenib to altered c-Raf protein and disassembles c-Raf from DAPK protein complex.
In another aspect, the present invention reveals the applications of any one of the abovementioned pharmaceutical compositions for treating cancer.
In another aspect, the present invention also provides methods for preparation of drugs that separate a protein complex using compounds, wherein at least one of the compounds can be used for dissociation of a protein complex and said protein complex consists of c-Raf (SEQ ID NO: 1) and DAPK (SEQ ID NO: 2).
According to the invention, the composition comprises sorafenib and GW5074.
In one aspect, the invention discloses a method for drug screening utilizing a biomarker and comprises a provided specimen and at least one of the following: the expression status and/or phosphorylation status of a biomarker prior to administration of the drugs. Drugs that are positively correlated with growth inhibition of cells after administration are deemed suitable drugs. The biomarker is selected from at least one of the following: protein c-Raf (SEQ ID NO: 1) and protein DAPK (SEQ ID NO: 2).
According to the invention, the phosphorylation site of c-Raf protein and DAPK protein is serine 338 (Ser338) and serine 308 (Ser308), respectively.
According to the invention, the specimen comprises ascites, blood, urine, feces, sputum, mucosal cells, gastric fluid, bile, or detached cancer tissues collected after a surgery.
According to the invention, the drugs are sorafenib and GW5074.
In one embodiment, the present invention also discloses the use of a biomarker for drug screening, wherein the biomarker is at least one of the following: protein c-Raf (SEQ ID NO: 1) and protein DAPK (SEQ ID NO: 2).
According to the invention, the phosphorylation site of c-Raf protein and DAPK protein is serine 338 (Ser338) and serine 308 (Ser308), respectively.
According to the invention, the drugs are sorafenib and GW5074.
According to the invention, the use further includes detection of at least one of the following: the expression status and phosphorylation status of the biomarker prior to administration of drugs, and those drugs that are positively correlated with growth inhibition observed after treatment are deemed suitable drugs.
The concept of the novel combination therapy is combining sorafenib, which is originally an antiangiogenic drug, with GW5074, which is a c-Raf inhibitor. When administered singularly at a low-dose (sorafenib at 5 uM or GW5074 at 10 uM), none of the two drugs showed growth inhibition. However, the combination of these two originally non-toxic drugs produced cytotoxicity, considerably reduced side effects resulting from an effective dose of sorafenib, as well as inhibited cancer cell growth. The novel combination therapy revealed in the present invention uncovers a unique molecular mechanism demonstrating that these two drugs destroy the protein complex of c-Raf and DAPK by binding to c-Raf, which in turn leads to cell apoptosis and can be used as new targets for future drug design. Studies indicated that the combination therapy was most effective in cancer cells with highly phosphorylated c-Raf s338, while exhibiting poor inhibition effects on human cancer cells with low DAPK protein expression or lower phosphorylated DAPK-s308.
The drug or drug for screening that dissociates c-Raf and DAPK proteins is a drug combination comprising sorafenib and GW5074.
The term “pharmaceutically acceptable excipient” is used herein to refer to any physiologically inert or pharmacologically inactive substance known to a person skilled in the art that is physically or chemically compatible with either sorafenib or GW5074. Pharmaceutically acceptable excipients include, but are not limited to, polymers, resins, plasticizers, fillers, lubricants, diluents, binders, disintegrants, solvents, cosolvents, surfactants, preservatives, sweeteners, flavoring agents, pharmaceutically grade dyes or pigments, and viscosity agents.
In this application, the term “pharmaceutical composition” is a solid or liquid composition whose form, concentration and degree of purity are suitable for administration to a patient (such as a human or an animal patient) and may induce desired physiological changes after its administration. A pharmaceutical composition is typically sterile and/or non-pyrogenic.
As used herein, the term “combination” describes materials that combining combine two or more compounds and/or drugs (also called ingredients in this application). The term “combined” and “combining” have the same meaning.
Binding of two or more compounds/drugs in a composition can be physical or non-physical. The examples of a compound/drug composition that was bound physically include compositions (e.g. a single mixture) that contains two or more mixed compounds/drugs (e.g. in the same single dosage), a composition that contains two or more chemically/physically-linked compounds/drugs (e.g. by cross-linking, molecular agglomeration or binding to a common vehicle moiety), a composition that contains two or more compounds/drugs that are chemically or physically co-packaged (e.g. formulated in a liquid medium, particles (e.g. micron particles or nanoparticles) or materials on or inside the emulsion droplets, pharmaceutical kits, pharmaceutical packs, or patient packs, wherein two or more compounds/drugs are co-packaged or co-represented (e.g. a batch of dosage units).
The examples of a compound/drug composition with non-physical binding include: a material (e.g. non-single mixture) that contains at least one of the two or more compounds/drugs plus the instructions indicating at least one or more physical bindings that can be used to generate two or more compounds/drugs, a material (e.g. non-single mixture) that contains at least one of the two or more compounds/drugs plus instructions demonstrating a combination therapy utilizing two or more compounds/drugs, a material which contains at least one of the two or more compounds/drugs plus instructions for administration to a patient population, wherein the patient population has been treated with (or is taking) the other drug (others) of the two or more compounds/drugs, and a material that comprises at least one of the two or more compounds/drugs whose amount or form is specially formulated to be used in composition with the other (others) of the two or more compounds/drugs.
In this application, the term “combination therapy” is used herein to refer to therapy using the composition containing two or more compounds/drugs (as defined above). Thus, in the present invention, “combination therapy,” “combination,” as well as “composition” of compounds/drugs are used to refer to compounds/drugs administered as part of the complete treatment. Consequently, the posology of each of the two or more compounds/drugs may be different, suggesting that each can be administered at the same or at different times. It is important to understand that the compounds/drugs of said composition may be given in order (e.g. before or after) or concurrently (e.g., at the same time), and may be formulated either in the same pharmaceutical mixture (together) or in different mixtures (separately). Furthermore, simultaneous administration in the same mixture is given as a single mixture, and simultaneous administration in different mixtures is not given as a single mixture. In addition, the posology of each of the two or more compounds/drugs in a combination therapy may also vary in accordance with ways of administration.
These features and advantages of the present invention will be fully understood and appreciated from the following detailed description of the accompanying Drawings.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1a shows growth inhibition of ACHN cells at 24, 48 and 72 hours after single-dose treatment of c-Raf inhibitors (sorafenib, GW5074, L779450 and PLX4720).
FIG. 1b shows growth inhibition of ACHN cells at 24, 48 and 72 hours after combination therapy of various c-Raf inhibitors (Sor: sorafenib, GW: GW5074, L77: L779450, PLX: PLX4720).
FIG. 2 shows the xenografted tumor volumes measured every 3 days for up to 21 days following sorafenib and GW5074 treatments administered singularly or in combination.
FIG. 3 shows the photon signals collected from the immunodeficient mice orthotopic xenografted with Luc-ACHN-LL cells following treatments of various drugs. To calculate the number of tumors distributed throughout the body, the total photons emitted from the entire body of each mouse was measured as well as quantified by Xenogen® living image software. The arrow indicates the time of initial drug administration.
FIG. 4a shows the status of apoptosis or necrosis of ACHN cells at 24 hours following treatments of DMSO (control group), 5 μM sorafenib and 10 μM GW5074 or combination therapy.
FIG. 4b shows the phosphorylation status of pDAPKS308 and DAPK protein expression of ACHN cells at 24 hours following treatments of DMSO (control group), 5 μM sorafenib and 10 μM GW5074 or combination therapy by immunoblotting.
FIG. 4c shows the immunoprecipitation results of endogenous DAPK (upper) and c-Raf (lower) of ACHN cells at 24 hours after treatments of DMSO (control group), 5 μM sorafenib and 10 μM GW5074 or combination therapy, followed by immunoblotting to stain other relevant proteins using specific antibodies.
FIG. 4d shows growth inhibition of ACHN cells following combination therapy in the presence or absence of PP2A inhibitor: cantharidin (C.A.) or okadaic acid (O.A.).
FIG. 4e shows growth inhibition of ACHN cells stably expressing wild-type or c-Raf mutants at 24 hours following combination therapy. (*p<0.05, **p<0.01 in comparison with wild type c-Raf).
FIG. 4f is a protein expression profile of ACHN cells expressing flag-tagged-c-Raf or indicated mutants at 24 hours following DMSO (Ctrl.) treatment or combination therapy. Flag-c-Raf was immunoprecipitated from the cell lysates, followed by immunoblotting for indicated antibodies.
FIG. 5a shows growth inhibition of ACHN, 786-O and Rcc-Sut-002 cells transfected with scrambled siRNA (Scr), DAPK siRNA1 (siDAPK-a), or DAPK siRNA2 (siDAPK-b) following combination therapy (upper panel). DAPK and α-catenin expression of the cell lysates were examined by immunoblotting (lower panel).
FIG. 5b shows growth inhibition of HeLa (left panel), MDA-MB231 cells expressing V5-tagged-DAP (right panel) and indicated mutants at 24 hours following combination therapy.
FIG. 5c shows growth inhibition of various cancer cells or normal cells at 24 hours following treatments of 5 μM sorafenib, 10 μM GW5074, or combination therapy. The lowest part indicates the phosphorylation status of pDAPKS308 of ACHN group in comparison with the control group. The expression of pDAPKS308 and DAPK was detected by immunoblotting.
FIG. 5d is a regression plot demonstrating the correlation between the expression of pDAPKS308 and growth inhibition of cells. R2=0.4551, R=0.6746, p=0.00001.
FIG. 6a shows the expression status of pDAPKS308 and DAPK in tumors (pT) or normal tissues (pN)(upper) of the same patient by immunoblotting. The lower panel indicates the relative intensity of pDAPKS308 after normalized to GAPDH expression.
FIG. 6b is the immnunohistochemical (IHC) analysis of pDAPKS308 expression of human normal and renal carcinoma tissues. Original magnification, ×40 (upper panel), ×100 (lower panel), scale bars is 100 μM.
FIG. 6c shows pDAPKS308 expression of human normal and renal cancer tissues after quantification using microarrays. The upper indicates normal as well as different grades (G), and the lower shows different stages (T) as well as metastasis of cancer cells (meta.).
FIG. 6d is a computer simulation photo demonstrating the conformation of c-Raf kinase after interaction with sorafenib and GW5074. Green represents GW5074 and magenta represents sorafenib.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
The present invention will now be described more specifically with reference to the following embodiments, which are provided for the purpose of demonstration rather than limitation.
EXAMPLE 1
Combination Therapy of Sorafenib and GW5074-Cell Testing
Human renal carcinoma (ACHN) cells were cultured in Eagle MEM (Minimum Essential Medium) with 10% FBS (Fetal Bovine Serum) and 1% penicillin/streptomycin. Sulforhodamine B (SRB) is a negative protein with a sulfonic acid group and binds to basic amino acids of intracellular proteins in weak acidic conditions. The SRB protein was extracted from cells using weak alkaline solution and then subjected to absorbance measurement. The amount of intracellular proteins, which is an indicator for cell survival, can be calculated from the amount of SRB. ACHN or A498 cells were treated singularly with 2.5 μM sorafenib, 5 μM sorafenib, 10 μM sorafenib, GW5074, L779450 or PLX4720 for 24, 48 and 72 hours, followed by SRB assay to assess cell survival. Alternatively, ACHN cells were pre-treated with 10 μM GW5074, 10 μM L779450 or 10 μM PLX4720 for 30 minutes prior to 5 μM sorafenib treatment for additional 24, 48 and 72 hours, followed by SRB assay to assess growth inhibition.
Based on the results, combination of c-Raf inhibitors comprising sorafenib and GW5074 showed no growth inhibition of cells following single low-dose treatment for 24 hours (5 μM sorafenib and 10 μM GW5074) (FIG. 1a, mean±S.D., n=4). However, combination of these two drugs not only induced cytotoxicity which was not observed in separate treatment of either drug originally, but successfully reduced side effects caused by effective dosage of sorafenib and inhibited cancer cell growth, suggesting a synergistic effect (FIG. 1b, mean±S.D., **P<0.01, n=4).
EXAMPLE 2
Combination Therapy of Sorafenib and GW5074-Xenograft
Six-week old immunodeficient male mice (BALB/cAnN.Cg-Foxn1nu/Cr1Nar1) with an average weight of 20 grams were xenografted with 1×107 ACHN cells to the right by intraperitoneal injection (i.p.). The mice were maintained in a specific pathogen-free (SPF) environment. The size of tumor was measured using a digital caliper twice a week and tumor volume was calculated by the equation of length*width*height*0.5. Drug administration which included 5 mg/kg sorafenib by oral gavage and subcutaneous injection of 10 mg/kg GW5074 once a day for three weeks was initiated when the tumor volume was >100 mm3, and the size of tumor was measured every three days. A total of four groups were included in the experiment: a control group which received only vehicle (DMSO), and test groups administered with 5 mg/kg sorafenib, 25 mg/kg GW5074, or combination therapy of 5 mg/kg sorafenib and 25 mg/kg GW5074, respectively, with 8 mice in each group.
The results are shown in FIG. 2. Separate treatment of either 5 μM sorafenib or 10 μM GW5074 exhibited nearly no inhibition effect. In contrast, combination therapy of 5 μM sorafenib and 10 μM GW5074 demonstrated significant growth inhibition of ACHN cells (t-test, mean±SD, **P<0.01, n=8).
EXAMPLE 3
Combination Therapy of Sorafenib and GW5074—The Orthotopic Model
To simulate clinical phenomenon, we established an orthotopic spontaneous animal model for studying metastasis of renal carcinoma. First, ACHN cells were transfected with luciferase gene and the resulted Luc-ACHN transfectants (stable transfectants which express luciferase) with different expression status were then selected for in vivo culture in mice by subcutaneous injection. Six-week old and shaved mice were subcutaneously injected with 1×107 Luc-ACHN cells in 0.1 ml PBS. Two months after injection, the mice were sacrificed and their kidneys, livers, regional lymph nodes as well as other organs were collected for assessing tumor cells that were potentially metastatic, which was confirmed by hematoxylin-eosin (H&E) staining. Tumor cell lines that are highly metastatic were dissected in 1 ml PBS into small pieces aseptically and then cultured in MEM media containing 10% FBS (fetal bovine serum) and 1% penicillin/streptomycin following centrifugation. A few days later, monoclonal cell lines were first treated with trypsin to dissociate the cells and then cultured in vitro. The cells obtained from liver tumor tissues were named ACHN-L. The metastatic potential of various monoclonal cell lines collected from different organs was further analyzed by xenografting these tumor cells to the left kidneys of mice. The xenografted mice were sacrificed and examined 8 weeks after injection of tumor cells. Tumor growth observed in each organ was investigated through visual examination and histology procedures. The metastatic cells found in the liver were dissected into small pieces aseptically and cultured in vitro. The cells obtained from liver tumor tissues were named ACHN-L (subcutaneous injection) cells and the cells collected from the metastatic lesions after injection of ACHN-L cells to the left kidneys were called ACHN-LL cells. The same procedure using orthotopic xenograft of ACHN-LL cells and liver metastatic cells was repeated twice to select for highly metastatic tumors. The cancer cell line (Luc-ACHN-LL), which is highly metastatic and causes high mortality, was selected. Immunodeficient male mice was injected with 3×105 Luc-ACHN-LL cells in 50 μL PBS at the right renal capsule. In vivo luciferase activity was examined every day for up to three weeks so as to assure no leakage of cancer cells at the kidneys immediately after injection and to monitor metastasis of these cancer cells. Two to five minutes before utilizing the IVIS Xenogene system, 75 mg/kg D-Luciferin (Xenogen) in PBS was injected to the retro-orbital sinus of each mouse. Two weeks after injection of Luc-ACHN-LL cells, IVIS Xenogene system was used to monitor transfer of biological fluorescent images and to calculate the intensities of the photon signals (photons/s/cm2/steradian). A total of five groups were included in the study: a control group which received only vehicle, and four test groups which respectively received 10 mg/kg sorafenib, 25 mg/kg GW5074, a combination therapy of 10 mg/kg sorafenib and 25 mg/kg GW5074 (the animals were fed with Sor 30 min post i.p. injection of GW), or 60 mg/kg sorafenib.
As shown in the results, the mice of the control group, 10 mg/kg sorafenib group, and 25 mg/kg GW5074 group died within 5, 8, and 5 weeks following injection of cancer cells, respectively. Likewise, loss of weight was also observed in the high-dose test group which received 60 mg/kg sorafenib, followed by death within 10 weeks. Surprisingly, only mice in the group which received low-dose combination therapy of 10 mg/kg sorafenib and 25 mg/kg GW5074 showed inhibition of both tumor sizes and metastasis of tumors as well as prolonged survival period in comparison with other groups. FIG. 3c shows the IVIS images and quantification of photon intensity, mean±SD, **P<0.01, n=4. In addition, the body weights as well as the energy of the mice that received combination therapy were similar to those observed in normal mice. The tumor cells collected from the mice which received combination therapy also showed profound cell necroptosis in comparison with other groups.
In summary, combination therapy of low-dose sorafenib and GW5074 is effective in growth inhibition of cancer cells in vitro. Also, most importantly, the efficacy of combination therapy can be examined in vivo in the condition which simulates clinical metastasis of cancer cells.
EXAMPLE 4
Combination therapy of sorafenib and GW5074 induces cell necroptosis through dephosphorylation of the death-associated DAPK at serine 308 followed by dissociation from proto-oncogene c-Raf. Cells were cultured as described in example 1, washed with phosphate buffered saline (PBS), and stained with annexin V-FITC and propidium iodide (PI) for 15 minutes. The presence of fluorescent Annexin V as well as propidium iodide (PI) was detected by flow cytometry so as to determine whether the cell death is caused by apoptosis or necrosis. The expression of c-Raf and DAPK as well as the phosphorylation status of DAPK were examined by Western blot and immunoprecipitation using antibodies. Anti-DAPK antibodies or non-immune rabbit IgG (IP: immunoglobulin) were included as negative controls, and cell survival was measured by SRB assay, as shown in example 1. In this experiment, ACHN cells were treated separately with DMSO (as a control group), 5 μM sorafenib, 10 μM GW5074, or combination therapy of 5 μM sorafenib and 10 μM GW5074 for 24 hours.
The results indicated that the average cell necroptosis rate of ACHN cells treated with DMSO, monotherapy of 5 μM sorafenib, and monotherapy of 10 μM GW5074 was 0.37, 0.77, and 1.35%, respectively. However, cells which received combination therapy showed significant increase of necroptosis, up to 53.95% (FIG. 4a, t-test, mean±SD, ***P<0.001, n=4). Significant decrease in phosphate groups of S308 due to dephosphorylation of pDAPKS308 by PP2A in tumor cells was only observed in cells treated with combination therapy (FIG. 4b). Results from immunoprecipitation further suggested c-Raf and DAPK, as well as PP2A, formed a complex. Combination therapy reduced the interactions among PP2A, DAPK and c-Raf, which subsequently decreased pDAPKS308 (FIG. 4c). For the test group which received combination therapy, various concentrations of PP2A inhibitors (Cantharidin acid, C.A. and Okadaic acid, O.A.) were effective in inhibition of dephosphorylation of pDAPKS308 and growth of ACHN cells only when provided 30 minutes prior to administration of the combination drugs (FIG. 4d, * P<0.05, ** P<0.01, n=4).
Next, the effects of combination therapy on the efficacy of pc-RafS338. Reduction of pDAPKS308 was noted as being most significant when ACHN cells were transfected with c-RafS338D (simulation of phosphorylating S338). Moreover, c-RafS338A (simulation of dephosphorylating S338) not only weakened dephosphorylation of DAPK S308, but also reduced growth inhibition of ACHN cells under combination therapy (FIG. 4e, * P<0.05, ** P<0.01, n=3). In addition, immunoprecipitation results suggested that c-RafS338D (simulation of phosphorylating S338) apparently lost its interaction with PP2A in comparison with c-RafWT (wilt type) and c-RafS338A (simulation of dephosphorylating S338) (FIG. 4f). Therefore, combination therapy not only increases pc-RafS338, but facilitates dephosphorylation of pDAPKS308 by PP2A and enhances cell necroptosis.
The above-mentioned example reveals that combination therapy of sorafenib and GW5074 induces cell necroptosis through dephosphorylating serine 308 of death-associated protein kinase (DAPK) followed by dissociation from proto-oncogene c-Raf. Disassembly of c-Raf and DAPK can also be used as the target for future drug design, which is dissociation of c-Raf from DAPK in cells leads to initiation of cell necroptosis process which kills cells effectively.
EXAMPLE 5
Methods of Drug Screening Using In Vitro Biomarkers
Previous studies showed that dephosphorylation of DAPK at serine 308 can be used as a predictive biomarker for anticancer effects of drugs on cancer cells. The methods for cell culture as well as detection for examining growth inhibition are as described in example 1. ACHN, 786-O and Rcc-Sut-002 (drug-resistant cancer cells) cell lines were treated with siRNA of type a and type b DAPK (siDAPK-a, sense strand: 5′-CAAGAAACGUUAGCAAAUGUU-3′ [SEQ ID No:3] and antisense strand: 5′-CAUUUGCUAACGUUUCUUGUU-3′ [SEQ ID No:4]; siDAPK-b, sense strand: 5′-GGUCAAGGAUCCAAAGAAGUU-3′ [SEQ ID No:5] and antisense strand 5′-CUUCUUUGGAUCCUUGACCUU-3′ [SEQ ID No:6]). Each cell line was analyzed by siDAPK-a, siDAPK-b and a control (Scr). Growth inhibition of cells was examined following combination therapy of 5 μM sorafenib and 10 μM GW5074 for 24 hr. On the other hand, HeLa cells and MDA-MB-231 cells were transfected with the control empty vector (vector), WT (wild type), DAPKS308D, DAPKS308A or DAPKK42A (inactivated protein kinase), and growth inhibition of the transfected cells was examined following combination therapy of 5 μM sorafenib and 10 μM GW5074 for 24 hours.
The results indicated that DAPK protein is indispensible for cytotoxicity induced by combination therapy of sorafenib and GW5074. In ACHN, 786-O and RCC-SUT-002 cells, growth inhibition resulting from two siRNAs capable of inhibiting DAPK expression was reduced by around 60% (FIG. 5a). Furthermore, phosphorylation of DAPK at S308 is highly associated with cytotoxicity induced by combination therapy. Overexpression of DAPKWT and DAPKS308D in HeLa cells which usually express higher pDAPKS308 notably increased the cytotoxicity after receiving combination therapy, whereas cell death was not enhanced in DAPKK42A (inactivated DAP kinase) and DAPKS308A (simulation of non-phosphorylation of S308) following combination therapy. Only DAPKS308D was found to increase growth inhibition in MDA-MB-231 breast cancer cells which usually express lower pDAPKS308 after receiving combination therapy. The rest, including DAPKWT, DAPKS308A, and DAPKK42A, showed no increase in growth inhibition (FIG. 5b, mean±SD, **p<0.01, n=3). According to the results, it is not the DAPK protein itself, but S308 phosphorylation of DAPK which plays a key role in inducing cytotoxicity when treated with combination therapy of sorafenib and GW5074. This is because dephosphorylation of S308 is not effective under combination therapy even with higher DAPK expression. The cytotoxicity effect induced by combination therapy must go through activated DAP K. Therefore combination therapy of sorafenib and GW5074 is only effective in the presence of pDAPKS308 in cancer cells.
Phosphorylation of c-Raf protein can be used as a biomarker for predicting the anticancer effect of drugs on cancer cells. Reduction of pDAPKS308 is most evident in ACHN cells transfected with c-RafS338D (simulating phosphorylation of S388). Not only does c-RafS338A (simulating dephosphorylation of S388) reduce dephosphorylation of DAPK S308, but also decreases growth inhibition of ACHN cells under combination therapy (FIG. 4e, * P<0.05, ** P<0.01, n=3). Thus, S338 phosphorylation of c-Raf is beneficial for combination therapy due to better treatment effects, and c-Raf S338D (simulating phosphorylation of S388) has a better effect in comparison with c-Raf S338A (simulating dephosphorylation of S388).
In addition, a number of cancer cells as well as normal cells were examined. It was found that combination therapy caused only limited cytotoxicity in the above-mentioned cells due to low S308 phosphorylation of DAPK in normal fibroblasts and epithelial cells. Nonetheless, growth inhibition caused by combination therapy among various tumor cells is positively correlated with the status of S308 phosphorylation of DAPK (FIGS. 5c and 5d, mean±SD, **p<0.01, n=3). It was further investigated as to whether combination therapy has an inhibition effect on drug-resistant cancer cells using sorafenib-resistant cancer cells obtained from clinical cases (RCC-Sut-001, RCC-Sut-002, RCC-Sor-001) and animal models (786-OT4, ACHN-T2R). All drug-resistant cancer cells that have highly phosphorylated DAPK S308 were significantly inhibited under combination therapy. Moreover, HT29 and A2058 cancer cell lines that are both Raf inhibitors-resistant showed high S308 phosphorylation of DAPK as well, and combination therapy demonstrated significant inhibition as well as synergistic effect (FIG. 5c and Table 1). Additionally, because S308 phosphorylation of DAPK in normal cells are relatively low, growth inhibition of cancer cells induced by combination therapy of sorafenib and GW5074 are therefore selective and cause no toxicity in normal cells.









TABLE 1







1
ACHN
renal cell adenocarcinoma


2
786-O
renal cell adenocarcinoma


3
A498
renal cell adenocarcinoma


4
LNCap
prostate carcinoma


5
22RV1
prostate carcinoma


6
PC-3
prostate carcinoma


7
DU-145
prostate carcinoma


8
MDA-453
breast adenocarcinoma


9
MCF-7
breast adenocarcinoma


10
MDA-231
breast adenocarcinoma


11
A549
lung carcinoma


12
H1299
non-small cell lung cancer


13
HepG2
hepatocellular carcinoma


14
HeLa
cervix carcinoma


15
A253
submaxiilary salivary gland carcinoma


16
U87
glioblastoma: astrocytoma


17
GBM8401
brain malignant glioma


18
LN229
glioblastoma


19
293T
kidney epithelial


20
3T3
embryo fibroblast


21
SV-HOC
uroepithelium epithelial


22
RWPE1
prostate normal epithelial cell


23
WPMY1
prostate normal epithelial cell


24
Colo-205
colorectal adenocarcinoma


25
HT-29
colorectal adenocarcinoma










26
A2058
melanoma
B-Raf mutation


27
ACHNC2
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell


28
ACHNT2R
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell


29
786-OC4
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell


30
786-OT4
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell


31
RCC-Sor-001
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell


32
RCC-Sut-001
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell


33
RCC-Sut-002
drug-resistant renal cell
Acquired resistant




adenocarcinoma cell









c-Raf and DAPK are found in cytoplasm and mitochondria. Combination therapy leads to relocation of DAPK between cytoplasm and mitochondria, along with dephosphorylation of pDAPKS308 by PP2A. Dephosphorylated DAPK decreases its interaction with c-Raf in cytoplasm. In addition, only DAPKS308D can be induced to be translocated from mitochondria to cytoplasm of MDA-MB-231 under combination therapy. This results in production of ROS and low phosphorylation of pDAPKS308. However, reduction of both c-Raf and phosphorylation of its S338 induced by combination therapy in cytoplasm and mitochondria was found only in cancer cells with highly phosphorylated pDAPK308 and not in cancer cells with low pDAPKS308.
EXAMPLE 6
The tumor samples and normal tissue samples collected from 20 patients with renal cell carcinoma were further investigated. Based on the Western blot results, 16 out of 20 samples showed elevated phosphorylation of DAPK at S308 in cancer cells in comparison with normal tissue samples (FIG. 6d. (pDAPKS308/GAPDH, mean±S.D., **p<0.005). Immnunohistochemical (IHC) analysis also demonstrated that S308 phosphorylation of DAPK was higher in 181 human renal carcinoma samples in comparison with normal kidney tissues (FIG. 6b). On the other hand, S308 phosphorylation of DAPK showed no significant differences between different grades (G) or stages (T) of the cancer using tissue microarray (TMA) and semi-quantitative analysis. The results suggested that pDAPKS308 is not only a factor for determining prognosis, but also a predictive biomarker of combination therapy for treating kidney cancers.
According to the results, a computer simulation experiment was then conducted to assess the crystal structures of various c-Raf inhibitors bound with c-Raf. The maximal energy was expected to be produced by binding of inhibitors to the structural region of c-Raf kinase when the combination of GW5074 and sorafenib binds to c-Raf (−182 kcal/mole, Table 2). GW5074 at the front end binds with c-Raf and produces a deeper hydrophobic pocket for binding through Ile355, Val363, Ala373, Leu406, Trp423 and Phe47. Under the circumstances, more regions in the hydrophobic pocket will be occupied by GW5074 and sorafenib (as shown in FIG. 6d).







TABLE 2







Various inhibitors bind to c-Raf separately or in combinations








Inhibitor
Binding energy









Name
Structure
(kcal/mole)





sorafenib




 −82


 


+L779450

−134


+GW5074

−125


+PLX44720

−113


 


GW5074




−128


 


+Sorafenib

−182


 


PLX44720




 −77


 


+sorafenib

−140


 


L779450




 −60


 


+sorafenib

−125









The present invention discloses a novel combination therapy for treating cancer by utilizing a composition that comprises sorafenib and GW5074. The combination therapy is not toxic to normal cells due to selective inhibition on cancer cells. Therefore, this therapy is safe and very promising for future applications. The efficacy of the combination therapy was verified by using pDAPKS308 as a predictive biomarker so as to avoid unnecessary treatments. The research of the present invention overcomes the obstacles faced by current studies for cancer therapies and meets the requirements of an ideal model for preclinical treatments.
Many changes and modifications in the above described embodiment of the invention can, of course, be carried out without departing from the scope thereof. Accordingly, to promote the progress in science and the useful arts, the invention is disclosed and is intended to be limited only by the scope of the appended claims.

## Claims

1. A method for the treatment of kidney cancer comprising the steps of;
detecting phosphorylation serine 308 of death-associated protein kinase (DAPK), and administrating an effective dosage of composition comprising sorafenib and GW5074 (3-(3,5-Dibromo-4-hydroxy-benzylidene)-5-iodo-1,3-dihydro-indol-2-one) to a subject in need thereof.

2. The method of claim 1, wherein the composition comprises further comprising pharmaceutically acceptable salts or vehicles.

3. The method of claim 2, wherein the vehicles include excipients, diluents, thickeners, fillers, binders, disintegrants, lubricants, oil or non-oil agents, surfactants, suspending agents, gelling agents, adjuvants, preservatives, antioxidants, stabilizers, coloring agents, or spices thereof.

4. The method of claim 1, wherein the composition is given by oral administration, immersion, injection, topical applications, or patch administration.