NZ622155B2 - Method of treating gastrointestinal stromal tumors - Google Patents

Abstract

The disclosure relates to a method of treating gastrointestinal stromal tumors (GIST), especially GIST, which is progressing after imatinib therapy or after imatinib and sunitinib therapy, using a combination comprising (a) a c-kit inhibitor selected from imatinib, nilotinib and masitinib or a pharmaceutically acceptable salt thereof; and (b) a PI3K inhibitor selected from 2-methyl-2-[4-(3-methyl-2-oxo-8-quinolin-3-yl-2,3- dihydro-imidazo[4,5-c]quinolin-1-yl)-phenyl]-propionitrile; 5-(2,6-di-morpholin-4-yl-pyrimidin-4-yl)-4-trifluoromethyl-pyridin-2-ylamine; and (S)-pyrrolidine-1,2-dicarboxylic acid 2-amide-1-({4-methyl-5-[2-(2,2,2-trifluoro-1,1-dimethyl-ethyl)-pyridin-4-yl]-thiazol-2-yl}- amide) or a pharmaceutically acceptable salt thereof. aceutically acceptable salt thereof; and (b) a PI3K inhibitor selected from 2-methyl-2-[4-(3-methyl-2-oxo-8-quinolin-3-yl-2,3- dihydro-imidazo[4,5-c]quinolin-1-yl)-phenyl]-propionitrile; 5-(2,6-di-morpholin-4-yl-pyrimidin-4-yl)-4-trifluoromethyl-pyridin-2-ylamine; and (S)-pyrrolidine-1,2-dicarboxylic acid 2-amide-1-({4-methyl-5-[2-(2,2,2-trifluoro-1,1-dimethyl-ethyl)-pyridin-4-yl]-thiazol-2-yl}- amide) or a pharmaceutically acceptable salt thereof.

Description

/061532 Method of Treating Gastrointestinal Stromal Tumors The present invention s to a method of treating gastrointestinal stromal tumors (GIST) in a human patient population using a combination comprising (a) a c-kit inhibitor and (b) a P|3K inhibitor or FGFR tor.

GIST are the most frequent mesenchymal tumors of the gastrointestinal tract. These tumors are thought to arise from the interstitial cells of Cajal, which compose the myenteric plexus found in the h and bowel. Primary GIST most frequently occur in the stomach (50- 60%), small bowel (20—30%), and large bowel (10%), with the esophagus, mesentery, omen- tum, and retroperitoneum accounting for the remaining cases. On the basis of population— based incidence rates in , it has been estimated that approximately 5000 new cases of GIST are diagnosed each year in the US. GIST predominantly occur in middle-aged and older people, with a median onset age of approximately 60 years and no apparent gender preference.

GIST may display a variety of phenotypic features, many of which correlate with patient prognosis. Thus, a consensus meeting emphasized tumor size and mitotic index for risk stratification of primary GIST, with such risk being correlated with tumor recurrence. At the present time, risk stratification based on pathologic criteria is preferable to the use of such terms as benign or malignant GIST. Patients with primary gastric GIST seem to fare slightly better than those with intestinal tumors. GIST have a tendency to recur both locally and in the form of peritoneal and liver ases, with node metastases being infrequent.

Surgical resection is the mainstay of therapy for primary GIST, and the disease is typically refractory to cytotoxic chemotherapy. The diagnosis of GIST has been facilitated by the dis- covery that these tumors stain positively with an immunohistochemical marker (CD1 17) pre- viously used to stain the titial cells of Cajal. The dy used in the immunohisto- chemical reaction recognizes the extracellular domain of the stem—cell factor receptor, KIT.

Currently, KIT expression is a major diagnostic criterion for GIST, and few other KIT-positive mesenchymal tumors of the gastrointestinal tract are likely to be confused with GIST; notable exceptions e metastatic melanoma and malignant vascular tumors. Approximately 95% of GIST stain positively for CD117. In most of these cases, somatic mutations can be found in the gene ng the KIT n, typically in exons 11, 9 and 13. These mutations confer PCT/U52012/061532 a gain of function to the receptor, which becomes constitutively activated regardless of the ce of .

The mainstay of therapy for patients with primary GIST is surgical resection. However, sur- gery alone is generally not curative; the 5—year disease specific survival is reported to be 54%. Recurrence rates exceeding 50% within 2 years of resection of primary GIST and ap- proximating 90% after re-excision, underscored the need for effective postoperative treat- ment. lmatinib received worldwide approval for the treatment of adult patients with KIT-positive (CD117) and ctable and/or metastatic GIST and dramatically changed the sis for such patients by ging the overall and the progression-free-survival (PFS) and in- creasing the 5-year survival rate. lmatinib at doses ranging from 400 mg/day to 800 mg/day is used worldwide for the treatment of ts with unresectable and/or metastatic KlT— positive GIST. In addition, imatinib 800 mg/day significantly improves progression-free sur- vival (PFS) in patients with advanced GIST harboring KIT exon 9 ons compared to 400 mgfday.

As a result of the efficacy of imatinib for the treatment of patients with unresectable and/or metatastatic GIST, a double-blind, randomized phase III study (ACOSOGZQOO1)was con— ducted to determine whether adjuvant treatment of adult ts with GIST following com- plete resection with 400 mg/day of imatinib for 12 months improved recurrence—free survival (RFS) compared with placebo. The results of the study indicated that treatment with imatinib significantly prolonged RFS. Based upon these data, imatinib at a dose of 400 mg/day was ed worldwide for adjuvant treatment of adult patients ing resection of GIST. Re- sults from SSGXVIIl/AIO, a Phase III multicenter, open-label, randomized study to assess the efficacy and safety of 400 mg imatinib once daily over 12 months or 36 months in GIST patients following surgery, and who were ted to be at high risk of disease recurrence are now available. The study data confirm that 36 months of adjuvant y with imatinib is well tolerated and superior to 12 months in ging RFS and overall survival in patients with GIST following surgical resection.

Despite the efficacy of imatinib, the treatment of metastatic GIST remains an area of unmet medical need with more than 50% of patients with advanced GIST ssing after 2 years of imatinib first line therapy.

Sunitinib t®; Pfizer), approved for use following progression on imatinib, is the only agent other than Glivec to be approved for the treatment of advanced unresectable GIST.

The agent has trated efficacy in patients who have progressed on imatinib therapy.

However, Sutent’s tolerability profile is a ng factor for long-term use in GIST.

It was now found that combining a KIT tor and inhibitors that target the survival path- ways in GIST can produce a greater therapeutic effect than that obtained by administration of a KIT inhibitor alone.

As shown herein, the FGF2 growth factor and its receptor FGFR1 are over-expressed in pri- mary GIST tissue, suggesting that FGFR pathway could be a survival pathway activated in GIST. FGFR1, but not FGF2, is over-expressed in GIST cell lines. However, the FGFR sig- naling pathway is activated in GIST cell lines in the presence of exogenous FGF2. In addi- tion, GIST cell lines are less sensitive to the treatment of KIT inhibitors in the ce of added FGF2. Combination of FGFR inhibitors with KlT inhibitors produces strong synergistic activity and significantly improved efficacy in the presence of FGF2 in GIST cells, suggesting that a combination comprising an FGFR tor and a KlT inhibitor can improve the efficacy of the current treatment gies in GIST.

In a broader sense, the present invention provides a method of treating GIST, preferably GIST not harboring any KIT mutations, by administering to a patient in need thereof a thera- peutically effective amount of a FGFR inhibitor. rmore, based on observations in GIST cell lines it was now surprisingly found that pa- tients with GIST progressing after ib first line therapy, might be treated sfully with a combination comprising (a) a c-kit inhibitor and (b) a PI3K inhibitor. rmore, it is concluded that patients with GIST progressing after consecutive therapy with imatinib and sunitinib can be treated successfully with a combination comprising (a) a c- kit inhibitor and (b) a P|3K inhibitor.

Hence, the present ion provides a method for treating GIST in a human patient progressing after imatinib therapy or consecutive imatinib and sunitinib y, sing co-administration to said patient, e.g., concomitantly or in sequence, of a therapeutically effective amount of (a) a c-kit inhibitor and (b) a PISK inhibitor or FGFR inhibitor. More broadly, the present invention provides a method for ng GIST in a human patient in need thereof, comprising co-administration to said patient, e.g., concomitantly or in sequence, of a therapeutically effective amount of (a) a c-kit inhibitor and (b) a PI3K inhibitor or FGFR inhibitor.

In a further aspect, the present invention relates to the use of a combination comprising (a) a c—kit inhibitor and (b) a PI3K inhibitor or FGFR inhibitor for the manufacture of a ment for the treatment of GIST, especially GIST progressing after imatinib first line therapy.

A further aspect of the ion relates to a combination comprising (a) a c—kit tor and (b) a PI3K inhibitor or FGFR inhibitor for the treatment of GIST, ally GIST progressing after imatinib therapy or GIST progressing after imatinib and sunitinib y.

In a further aspect, there is provided a use of a c-kit inhibitor selected from the group consisting of imatinib, nilotinib and masitinib, or a pharmaceutically acceptable salt thereof, respectively, and a PI3K inhibitor selected from the group consisting of 2—methyl-2—[4-(3— methyl-2—oxo—8-quinolin—3-yl-2,3—dihydro-imidazo[4,5-c}quinolinyl)-phenyI]-propionitrile, 5- i-morpholin—4—yI-pyrimidin—4-yI)-4~trif|uoromethyI—pyridin—2—ylamine, and (S)—pyrrolidine- 1,2—dicarboxylic acid 2—amide 1~({4~methyl[2—(2,2,2—trifluoro—1,1~dimethyI-ethyl)-pyridin yli-thiazoIyI}—amide), or a pharmaceutically acceptable salt thereof, respectively, in the manufacture of a medicament for the treatment of gastrointestinal stromal tumors .

In a further aspect, there is provided a combination comprising (a) a c—kit inhibitor selected from the group consisting of imatinib, nilotinib and masitinib, or a pharmaceutically acceptable salt thereof, respectively, and (b) a PI3K inhibitor selected from the group consisting of 2-methyl-2—[4-(3-methyl-2—oxo-8—quinolinyI-2,3-dihydro—imidazo[4,5- oliny|)-phenyl]-propionitrile, 5-(2,6-di-morphoiin-4—yl-pyrimidinyl)trifluoromethyi- pyridinylamine, and (S)-pyrrolidine-1,2-dicarboxylic acid 2—amide 1-({4-methyl[2-(2,2,2- [followed by page 4a] oro-1,1-dimethyl-ethyl)—pyridinyI}—thiazolyI}-amide), or a pharmaceutically acceptable salt thereof, respectively, adapted for the treatment of gastrointestinal stromal tumors (GIST).

Short Description of the Figures Figure 1: FGF2 and FGFR1 are highly expressed in primary GISTs. Raw data (CEL files) of the expression es for 30,094 primary tumors were normalized by MASS algorithm using 150 as the target value.

Figure 2: FGF2 expression is substantially higher in KIT-positive primary gastrointestinal stromal tumors (GISTs) than in other human primary tumor tissues. GAPDH Western blot is shown as a loading control.

Figure 3: FGFR y is activated in GIST cell lines in the presence of various concentrations of added FGF2. FRSZ Tyr-Phosphorylation was used as the readout of FGFR signaling activation and measured by Western blot in the GIST cell lines. Total FRSZ level is shown as the loading l.

Figure 4: GIST cell lines are less sensitive to the treatment of a KIT inhibitor AMN107 (nilotinib) in the ce of added FGF2. GIST—T1 and GIST882 cell lines were treated with [followed by page 5] PCT/U82012/061532 AMN107 for 3 days with serial dilutions of the KIT inhibitor AMN107 in the absence or pres- ence of 50 ng/ml, 25 ng/ml, 12 ng/ml FGF2. Relative cell growth was measured by Cell Titer Glo assay and expressed as a percentage of DMSO-treated cells.

Figure 5: Combination effect of imatinib plus BGJ398 in GIST-T1 and GIST882 in the ab- sence and of presence of 20 ng/ml FGF2. The left panels show the percent inhibition relative to reated cells for each single agent and combination treatments. sing concen- trations of imatinib (CGP05714BB) are shown along the left column from bottom to top and increasing concentrations of BGJ398 along the bottom row from left to right. The middle pan- els show the excess inhibition for each point in the left . Excess inhibition was deter- mined based on the Loewe synergy model that measures the effect on growth ve to what should be expected if the two drugs only function vely. Positive numbers indicate synergy, and negative numbers antagonism. The right panels are the isobolograms that dis- play the interactions between the two compounds. The red straight lines connecting the dos- es of imatinib and BGJ398 represent the additive effect. Blue curves that lie below and to the left of the ht lines represent synergism.

Figure 6: Combination effect of nilotinib plus BGJ398 in GIST cell lines in the presence of 20 ng/ml FGF2.

The expression “c-kit inhibitor” as used herein includes, but is not limited to, 4-(4- methylpiperazinylmethyl)—N-[4—methyl-3—(4—(pyridinyl)pyrimidinylamino)phenyl]— benzamide (lmatinib), 4-methyl—3-[[4—(3-pyridinyl)—2—pyrimidinyl]amino]-N-[5-(4—methyl~lH- imidazolyl)(trifluoromethyl)phenyl] benzamide (Nilotinib), masitinib, sunitinib, sorafenib , regorafeinib, motesanib, and, respectively, the pharmaceutically acceptable salts thereof.

In a preferred embodiment the c-kit inhibitor employed is lmatinib. lmatinib is specifically dis~ closed in the patent ations US 5,521,184, the subject—matter of which is hereby incorpo- rated into the t application by reference. lmatinib can also be prepared in accordance with the processes disclosed in W003/066613. For the purpose of the present invention, lmatinib is preferably applied in the form of its mono-mesylate salt. lmatinib mono-mesylate can be prepared in accordance with the processes disclosed in US 6,894,051. Comprised by the present ion are likewise the corresponding polymorphs, e.g. crystal cations, which are disclosed in US 6,894,051. in a further preferred embodiment of the method described herein the mono-mesylate salt of lmatinib is administered orally in dosage forms as described in US 5,521 ,184, US 6,894,051 or US 2005-0267125. The te salt of lmatinib is marketed under the brand Glivec® (Gleevec®). A preferred oral daily dosage of lmatinib is 200 - 600 mg, in particular 400 mg/day, administered as a single dose or divided into multiple doses, such as twice daily dosing.

In a r preferred ment of the present invention, the c—kit inhibitor employed is Ni- lotinib. Nilotinib and the process for its manufacture are disclosed in WC 04/005281, which is hereby incorporated into the present ation by reference. Pharmaceutically acceptable salts of nib are especially those disclosed in WO2007/015871. For the e of the present invention, nib is preferably applied in the form of its mono-hydrochloride mono- hydrate salt. WO2007/015870 ses certain polymorphs of nib and its pharmaceutically acceptable salts useful for the present invention.

In a further red embodiment of the method described herein the mono-hydrochloride salt of Nilotinib is administered orally in dosage forms as described in W02008l037716. The mono-hydrochloride salt of Nilotinib is marketed under the brand Tasigna®. A preferred oral daily dosage of Nilotinib is 200 - 1200 mg, e.g. 800 mg, administered as a single dose or di- vided into multiple doses, such as twice daily .

The phosphatidylinositol 3-kinases (Pl3Ks) are a family of lipid kinases which phosphorylate the 3'-OH group of phosphatidylinositols in the lumen side of the cell membrane, and are in- volved in the regulation of a wide range of cellular ses. In response to lipid ory- lation (Png to PIP3) various signaling proteins, including the protein serine-threonine kinase AKT, are recruited to the plasma membrane, where they become activated and initiate a sig- nal transduction cascade.

There are three classes of Pl3Ks (HM), and currently 8 members of the family are known.

The class l enzymes consist of heterodimers having a regulatory (p85) domain and a catalyt- ic (p1 10) subunit, of which there are four isoforms: p1100i, p1 1013, p110?) and p110\(. The d and [3 isoforms are ubiquitously expressed; a is linked upstream mainly to receptor tyrosine kinases, whereas 8 can mediate signals from both G-protein-coupled receptors and from re- PCT/U82012/061532 ceptor tyrosine s. The 6 and y isoforms are expressed primarily in lymphocytes and play important roles in the regulation of immune responses. The v isoform is also highly ex- pressed in GIST. However, the function of v isoform in GIST is still unknown.

A gain of function in Pl3K ing is common in many types of human cancer and include inactivation of the PTEN tumor suppressor gene, amplification/overexpression or activating mutations of some receptor tyrosine kinases (e.g. erbB3, erbBZ, EGFR), amplification of ge- nomic regions containing AKT, amplification of PIK3CA (the gene encoding p110cx) and mu— tations in p110a. More than 30% of various solid tumor types were recently found to contain mutations of PIK3CA. From these mutation frequencies, PIK3CA is one of the most common- ly mutated genes identified in human cancers.

The expression “Pl3K inhibitor” as used herein includes, but is not limited to those specified below, W02006/122806 describes imidazoquinoline derivatives, which have been described to in- hibit the activity of lipid s, such as Pl3-kinases. Specific imidazoquinoline tives which are suitable for the present invention, their ation and suitable pharmaceutical formulations ning the same are described in W02006/122806 and include nds of formula I R1 R2 \ ’( / N\R3 R5 T R7 (R6)n (I), wherein R1 is naphthyl or phenyl wherein said phenyl is tuted by one or two substituents inde- pendently selected from the group ting of Halogen; lower alkyl unsubstituted or substi- tuted by halogen, cyano, imidazolyl or triazolyl; cycloalkyl; amino substituted by one or two PCT/U52012/061532 substituents independently selected from the group consisting of lower alkyl, lower alkyl sul- fonyl, lower alkoxy and lower alkoxy lower alkylamino; piperazinyl unsubstituted or tut- ed by one or two substituents independently selected from the group consisting of lower alkyl and lower alkyl sulfonyl; 2—oxo-pyrrolidinyl; lower alkoxy lower alkyl; olyl; pyrazolyl; and lyl; R2 is O or 8; R3 is lower alkyl; R4 is pyridyl unsubstituted or substituted by n, cyano, lower alkyl, lower alkoxy or pi- perazinyl unsubstituted or substituted by lower alkyl; pyrimidinyl unsubstituted or substituted by lower alkoxy; quinolinyl unsubstituted or substituted by halogen; quinoxalinyl; or phenyl substituted with alkoxy R5 is hydrogen or halogen; n is 0 or 1; R6 is oxido; with the proviso that if n=i, the N-atom bearing the l R6 has a positive charge; R7 is hydrogen or amino; or a tautomer thereof, or a pharmaceutically able salt, or a hydrate or solvate thereof.

The radicals and symbols as used in the definition of a compound of a I have the meanings as disclosed in W02006/122806 which publication is hereby incorporated into the present application by reference.

A red compound of the present invention is a compound which is specifically described in W02006/122806. A very preferred compound of the present invention is 2-methyl—2—[4-(3- methyloxo-8—quinolinyl-2,3-dihydro—imidazo{4,5-c]quinolinyl)—phenyl]—propionitrile and its monotosylate salt (COMPOUND A). The synthesis of 2-methyl-2—[4-(3-methyloxo—8— quinolin—3-yl—2,3-dihydro—imidazo[4,5~c]quinolin—1-yl)-phenyl]~propionitrile is for instance de- scribed in W02006/122806 as Example 1. r very preferred compound of the present invention is 8-(6-methoxy-pyridin-3—yl)methyl(4-piperazin-i—yltrifluoromethyl-phenyl)- 1,3-dihydro—imidazo[4,5-c]quinolinone (COMPOUND B). The synthesis of 8-(6-methoxy— pyridinyl)—3-methyl(4-piperazinyltrifluoromethyl-phenyl)—1 ,3-dihydro-imidazo[4,5- clquinolin-Z-one is for instance described in W02006/122806 as Example 86. 2012/061532 WOO7/084786 describes dine derivatives, which have been found the activity of lipid kinases, such as Pl3-kinases. Specific pyrimidine derivatives which are suitable for the pre- sent invention, their preparation and suitable pharmaceutical formulations containing the same are described in WOW/084786 and include compounds of formula I HNZYIRaRZw N\ R1 R4 N N 0 II or a isomer, tautomer, or pharmaceutically acceptable salt thereof, wherein, W is CRw or N, wherein Rw is ed from the group consisting of (1) hydrogen, (2) cyano, (3) halogen, (4) methyl, (5) trifluoromethyl, (6) sulfonamido; R1 is selected from the group consisting of (1) hydrogen, (2) cyano, (3) nitro, (4) halogen, (5) substituted and unsubstituted alkyl, (6) substituted and unsubstituted alkenyl, (7) substituted and unsubstituted alkynyl, (8) substituted and unsubstituted aryl, (9) substituted and unsubstituted aryl, (10) substituted and unsubstituted heterocyclyl, ) substituted and unsubstituted lkyl, (12) -COR1a, ) ~CozR1a, PCT/U82012/061532 (14) -CONR1aR1b, (15) -NR1aR1b, (16) ‘NR1aCOR1b: (17) -NR1aSOQR1b, (18) -OCOR1a, (19) 'OR1a; (20) “SR1a; (21) -SOR1a, (22) a, and (23) -SOgNR1aR1b, wherein R13, and R“, are independently selected from the group consisting of (a) hydrogen, (b) substituted or unsubstituted alkyl, (c) substituted and unsubstituted aryl, (d) substituted and unsubstituted heteroaryl, (e) substituted and unsubstituted heterocyclyl, and (f) substituted and unsubstituted cycloalkyl; R2 is selected from the group consisting (1) en, (2) cyano, (3) nitro, (4) halogen, (5) hydroxy, (6) amino, (7) substituted and unsubstituted alkyl, (8) -COR2a, and (9) -NR23COR2b, wherein R23, and Rgb are independently selected from the group ting of (a) hydrogen, and (b ) substituted or unsubstituted alkyl; R3 is selected from the group consisting of (1 ) hydrogen, ( ) cyano, ( (ION ) nitro, (J; ) halogen, (5) substituted and unsubstituted alkyl, (6) substituted and unsubstituted alkenyl, (7) substituted and unsubstituted alkynyl, (8) substituted and unsubstituted aryl, (9) tuted and unsubstituted heteroaryl, (10) substituted and unsubstituted heterocyclyl, (11) substituted and unsubstituted cycloalkyl, (12) -COR3a, (13) 3b, (14) -NR3aCOR3b, (15) OzR3b, (16) —OR33, (17) -SR3a, (18) ‘SORBa: (19) -SOZR33, and (20) 33R3b, wherein R33, and R3,, are independently selected from the group consisting of (a) en, (b) substituted or unsubstituted alkyl, (c) tuted and unsubstituted aryl, (d) substituted and unsubstituted heteroaryl, (e) substituted and unsubstituted heterocyclyl, and (f) substituted and unsubstituted cycloalkyl; andR4 is selected from the group consisting of (1) hydrogen, and (2) halogen.

The radicals and symbols as used in the definition of a compound of formula I have the meanings as disclosed in WOW/084786 which publication is hereby incorporated into the present application by reference.

A preferred compound of the present invention is a compound which is specifically described in WOW/084786. A very preferred compound of the present invention is 5-(2,6-di-morpho|in- 4-yl-pyrimidinyl)—4-trifluoromethyI-pyridin-Z—ylamine UND C). The synthesis of 5- PCT/U52012/061532 (2,6-di-morpholinyl-pyrimidin-4—yl)-4—trifluoromethyl-pyridinylamine is described in WOW/084786 as Example 10.

A further preferred P|3K inhibitor of the t invention is (S)-pyrrolidine-1,2-dicarboxylic acid 2—amide 1-({4-methyl-5—[2~(2,2,2—trifluoro—1,1—dimethyl-ethyl)-pyridin—4—yl]—thiazoI-Z-yl}- amide) (COMPOUND D) or a pharmaceutically acceptable salt thereof. The sis of (S)— Pyrrolidine—1,2-dicarboxylic acid 2-amide 1-({4~methyl—5-[2—(2,2,2—trifluoro—1,1-dimethyI-ethyl)- pyridinyI]-thiazolyI}-amide) is for instance described in as Example The expression “FGFR inhibitor” as used herein includes, but is not limited to (a) ib, intedanib, E-7080, ponatinib, SU-6668 and AZD-4547. (b) the compounds disclosed in W02009/141386, and (c) W02006/000420 (including 3-(2,6—dichIoro—3,5-dimethoxy—phenyl){6-[4-(4-ethylpiperaziny |)-phenylamino]-pyrimidyl}methyI-urea monophosphate, BGJ398). BGJ398 is a pan-FGFR kinase inhibitor inhibiting FGFR 1-3 (IC5O between 3 and 7 nM).

The following aspects of the invention are of particular importance: (1 .) A method of treating GIST in a human patient comprising stering to the human pa- tient in need thereof a dose effective against GIST of a combination (a) a c—kit inhibitor and (b) a P|3K tor or FGFR inhibitor, or a pharmaceutically acceptable salt thereof, respectively, especially n the c-kit inhibitor is selected from imatinib, nilotinib and masitinib, or, respectively, a ceutically acceptable salt thereof. (2.) A method of treating GIST in a human patient comprising administering to the human pa- tient in need thereof a dose effective against GIST, wherein the GIST is progressing after ib therapy or after imatinib and sunitinib therapy. (3.) A combination sing (a) a c-kit inhibitor and (b) a PI3K inhibitor or FGFR inhibitor or a pharmaceutically acceptable salt thereof, respectively, for the ent of GIST.

For the purposes of the present invention, a combination comprising (a) a c-kit inhibitor and (b) a PI3K inhibitor or FGFR inhibitor is preferably selected from (1) imatinib or a pharmaceutically able salt thereof and COMPOUND A or a pharma- ceutically acceptable salt thereof, PCT/U82012/061532 (2) imatinib or a pharmaceutically acceptable salt thereof and COMPOUND C or a pharmaceutically acceptable salt thereof, (3) imatinib or a pharmaceutically acceptable salt thereof and COMPOUND D or a pharma— ceutically acceptable salt thereof, (4) masitinib or a pharmaceutically acceptable salt thereof and COMPOUND A or a pharma- ally acceptable salt thereof, (5) masitinib or a pharmaceutically acceptable salt thereof and COMPOUND C or a pharma- ceutically acceptable salt thereof, and (6) masitinib or a pharmaceutically acceptable salt thereof and COMPOUND D or a pharma- ceutically acceptable salt thereof, (7) imatinib or a pharmaceutically acceptable salt thereof and BGJ398 or a pharmaceutically acceptable salt thereof, (8) nib or a pharmaceutically able salt thereof and BGJ398 or a pharmaceutically acceptable salt thereof, (9) nilotinib or a pharmaceutically acceptable salt f and BGJ398 or a ceutically acceptable salt thereof, (10) imatinib or a pharmaceutically acceptable salt thereof and FGFR inhibitor selected from brivanib, intedanib, E-7080, ponatinib, SU-6668 and AZD—4547. (11) a c—KlT inhibitor selected from sunitinib, sorafenib motesanib or a phar- , regorafenib , maceutically able salt thereof, respectively, and COMPOUND A or a pharmaceutically acceptable salt thereof, (12) a c-KIT inhibitor selected from nib, sorafenib or a phar- , regorafenib , motesanib maceutically acceptable salt thereof, respectively, and COMPOUND C or a pharmaceutically acceptable salt thereof, (13) a c—KIT inhibitor selected from sunitinib, sorafenib motesanib or a phar- , regorafenib , maceutically acceptable salt thereof, respectively, and COMPOUND D or a pharmaceutically acceptable salt f, and (14) a c-KIT inhibitor selected from sunitinib, sorafenib a phar- , regorafenib , motesanib or maceutically acceptable salt thereof, respectively, and BGJ398 or a ceutically ac- le salt thereof.

For the purposes of the t invention, the PlSK tor is ably ed from 2-methyl-2—[4-(3-methyloxo-8—quinolinyl-2,3-dihydro-imidazo[4,5-c]quinolinyl)- phenyl]-propionitrile, 5-(2,6—di—morpholinyI-pyrimidinyl)trifluoromethyl-pyridin-Z- 2012/061532 ylamine, and (S)-pyrro|idine-1,2-dicarboxylic acid 2-amide 1-({4-methyI[2-(2,2,2-trif|uoro- 1,1-dimethyl—ethyI)-pyridin-4~yl]—thiazo|—2-yi}-amide), or, respectively, a pharmaceutically acceptable salt thereof.

The structure of the active agents identified by generic or trade names may be taken from the actual edition of the standard compendium “The Merck index” or from ses, e.g.

Patents international (e.g. lMS World Publications). The corresponding content thereof is hereby incorporated by reference.

Unless mentioned ise, the P|3K inhibitors, c—KlT inhibitors and FGFR inhibitors are used in a dosage as either specified in the product information of a product comprising such inhibitor for the ent of a proliferative disorder, or, especially if such product information is not available, in a dosage which is determined in dose finding studies.

Suitable clinical studies in human patients are, for example, open label non-randomized, studies in patients with GIST progressing after imatinib first line therapy. Such studies prove in ular superiority of the d method of ent compared to treatments with one of the components of the treatment schedule alone. The beneficial effects on GlST can be determined directly through the results of these studies (e.g. RFS or progression free survival - PFS) or by changes in the study design which are known as such to a person skilled in the art.

PCT/U82012/061532 Examples The following Example illustrates the invention described above, but is not, however, intend- ed to limit the scope of the invention in any way. Other test models known as such to the person skilled in the ent art can also determine the beneficial effects of the claimed in- vention.

Example 1 - FGF receptor 1 (FGFR1) and FGF2 sion in grimam GlSTs Cell lines and culture GlST882, GIST48 and GlST430 cell lines were ed from the Brigham and Women’s Hospital, Boston, MA. GlST882 was established from an untreated human GIST with a ho- mozygous se mutation in KlT exon 13, ng a K642E mutant KIT protein (Tuveson DA, Willis NA, et al. Oncogene 2001; 20: 5054—5058). GIST48 and GIST430 were established from GISTs that has ssed after initial clinical se to imatinib treat- ment (Bauer 8, Yu LK, Demetri GD, Fletcher JA. Cancer Res 2006; 66: 9153—9161). GlST48 has a primary homozygous exon 11 missense mutation (V560D) and a secondary heterozy- gous exon 17 missense mutation (D820A). GIST430 has a primary heterozygous exon 11 in- frame deletion and a secondary heterozygous exon 13 missense mutation ). GIST-T1 was obtained from Kochi Medical School, Kochi, Japan. it was established from a metastatic human GIST with a heterozygous deletion of 57 bases in exon 11 of KIT (Taguchi T, Sonobe H, Toyonaga S, et al. Lab Invest 2002; 82: 5).

GIST882 cells were cultured in RPMl-164O (ATCC Catalog # 30-2001) supplemented with % FBS and 1% L—glutamine, GIST48 cells in F10 (Gibco/lnvitrogen Catalog # 11550-043) supplemented with 15% FBS, 0.5% Mito+ (BD Bioscience Catalog # 355006), 1% BPE (BD Bioscience/Fisher Catalog# 354123) and 1% L-glutamine, 0 cells in lMEM (Gib- co/lnvitrogen Catalog # 12440-053) supplemented with 15% FBS and 1% L-glutamine, and 1 cells in DMEM (Gibco/lnvitrogen Catalog # 11965) supplemented with 10% FBS.

Cell viability assay WO 63000 Imatinib and BGJ398 were dissolved in DMSO as a 10 mM stock, and subsequently diluted with media to make a series of working solutions at concentrations (pM) of 0, 0.02, 0.05, 0.16, 0.49, 1.48, 4.44, 13.3 and 40. 10,000 cells suspended in 80 pl media were seeded into each well of a 96-well cell-culture plate and grown for 24 hours prior to treatment. 10 pl of 60 pg/mL heparin (Sigma Catalog # H3149) was added to each well, and then 10 pl of 50 pg/mL FGF2 (R&D Catalog # /CF) or media was added to each well of the plates. 10 pl of each of the compound dilutions described above and 10 pl of media were added to wells to a final volume 120 pl such that all pair-wise ations as well as the single agents were represented. Cells were incubated for 72 hrs at 37°C in a 5% CO2 incubator following com— pound on. Cell proliferation was measured using the CellTiter—Glo luminescent cell via- bility assay (Promega catalog # G755B) and Victor4 plate reader (Perkin Elmer). Synergy scores and C|70 calculations were determined as bed elsewhere (Lehar J, r AS, et al. Nat Biotechnol 2009; 27: 659-666).

Western blotting n lysates Were prepared from cell monalayers using RIPA buffer (Cell Signaling Tech- nology Catalog # 9806) according to the procedure described by the manufacturer. Antibod- ies to detect o-KIT (Catalog # 30738), total KIT (Catalog # 3308), phospho-AKT S473 (Catalog # 4058), total AKT (Catalog # 9272), phospho-ERK (Catalog # 9101), total ERK (Catalog # 9107) and phospho-FRS2 (Catalog # 3864) were purchased from Cell Signaling Technology. Antibody to GAPDH (Catalog # MAB374) was purchased from Millipore and an— ti-FRS2(H-91) (Catalog #sc-8318) from Santa Cruz. Bound antibody was detected using the Ll-COR Odyssey ed Imaging System.

Results is OncExpress database contains both internally and publically deposited expression data for 30,094 primary tumors, including 110 GIST samples, profiled by Affymetrix Human Genome U133A or U133 Plus 2.0 arrays. In addition to the known GIST—specific genes, such as KIT, ETV1 and PRKCQ, FGF2 and its or FGFR1 showed the highest average ex- pression levels in GIST among 41 tumor types included in this dataset (Figure 1), ting that FGFR pathway could be a survival pathway in GIST. FGF2 was also found to be over- expressed at the protein level in primary GlSTs (Figure 2). FGFR1, but not FGF2, is over- WO 63000 2012/061532 expressed in GIST cell lines. However, the FGFR signaling pathway was activated when var- ious concentrations of exogenous FGF2 was added (Figure 3).

GIST-T1 and GlST882 are sensitive to KIT inhibition achieved by nilotinib (AMN107) treat— ment e 4). However, these two cell lines were shown to be less sensitive to KIT inhibi- tion in the presence of added FGF2 with the Gl5o values shifted greater than 10 fold (Figure 4), suggesting that FGFR signaling can function as a survival pathway once ted. There fore, combining a KIT inhibitor and a potent FGFR inhibitor should enhance the growth inhibi- tion in the GIST cell lines.

BGJ398 is an orally active, potent and selective inhibitor of FGFRs. To determine the single agent and combination s of combining the FGFR inhibitor BGJ398 and the KlT inhibitor ib (CGP05714SB) on the growth inhibition of GIST cells, we compared the proliferation responses for cells treated with dose ranges of each nd alone and pair-wise combi- nations for 3 days. As a single agent, imatinib was efficacious in inhibiting GIST-T1 and GIST882 growth in the e of FGF2 (Figure 5). In the presence of added FGF2, these two cell lines were less sensitive to imatinib treatment (Figure 5), similar to the results shown in Figure 4. BGJ398 did not significantly affect the viability of GIST cell lines, either in the presence or the absence of FGF2 (Figure 5). However, BGJ398 combination with a KIT in- r nib or nilotinib) resulted in strong combination effects in the presence of FGF2 in GIST cells. Combination effects were shown in Figure 5 and determined by combination indi- ces at a 70% inhibitory effect (Cl7o) that measure dose shifting yielding 70% growth inhibition and by synergy scores that measure overall synergy observed across the entire dose matrix- es (Lehar J, Krueger AS, al. Nat Biotechnol 2009; 27: 659-666).

Also the combination of nilotinib and BGJ398 shows synergy in GIST cell lines even in the presence of FGF2 (Figure 6).

Conclusion The expression profiles of more than 30,000 primary tumors show that FGF receptor 1 (FGFRI) and its ligand, FGF2, are highly sed in primary GlSTs, suggesting that the FGFR y is activated in GlSTs. In addition, the FGFR pathway, when activated, can function as a survival pathway in GIST cell lines, making them less sensitive to KIT inhibition.

PCT/U52012/061532 —18- However, combining FGFR tors with KIT inhibitors resulted in strong synergistic and ro- bust inhibition of the growth of GIST cell lines and restored complete growth inhibition by imatinib inhibition. These results t that a combination comprising an FGFR inhibitor and a KlT inhibitor can e the current therapeutic strategy in GIST.

Examgle 2 — Effects of imatinib in combination with PI3K inhibitors on the growth of GIST cell lines The effects of COMPOUND A, COMPOUND C, COMPOUND D and of imatinib have been evaluated both as single agents and in combination in patient-derived GIST882 (expressing K642E mutant KIT), GIST48 (expressing V560D/D83OA KIT), GIST430 (expressing ex11del/V654A KIT) and GIST—T1 (expressing ex11de| KIT) cell lines. As single agents imatinib potently inhibited the proliferation of the GIST882, GIST430 and GIST-T1 cell lines (GIST48 being imatinib resistant) and COMPOUND A and COMPOUND C inhibited the pro- liferation of all four cell-lines at low olar concentrations, whereas COMPOUND D showed little or no effect on the proIiferation of any of the cell-lines. When the antiproliferative effects of imatinib and COMPOUND A were ted in ation, growth suppression was observed in excess of the percent inhibition achieved by imatinib or COMPOUND A sin- gle agent treatment in GIST882 and GIST430 ceIi~lines. When the antiproliferative effects of imatinib and COMPOUND C were evaluated in ation, growth suppression was ob- served in excess of the percent inhibition achieved by imatinib or COMPOUND C single agent treatment in both the GIST882 and GIST430 cell-lines. When the antiproliferative ef- fects of imatinib and COMPOUND D were ted in combination, growth suppression was ed in excess of the t inhibition achieved by imatinib or COMPOUND D single agent treatment in the imatinib insensitive GIST48 and GIST430 cell-lines.

Labial 2012/061532 bined with GIST882 GIST-T1 GIST48 GIST430 COMPOUNDA 0.194 0.493 0.260 COMPOUNDC 0.597 0.782 0.252 Synergy is quantified either as the ‘weighted’ Synergy Score, 8 (where S s 1 indicates either some additivity or no cooperativity or, S > 1 suggests of some synergy and S > 2 indicates significant synergy) or as Combination Indices, CI (where CI = 1 tes dose additivity, CI < 0.5 indicates “real" synergy (2x dose shift), Cl < 0.3 indicates “useful” synergy (3x shift) and CI < 0.1 indicates "strong” synergy (10x shift). Significant assessments of synergy are indi- cated in bold-type.

Example 3: Single-arm dose-finding phase lb study of ib in combination with the oral phosphatidyl-inositol 3-kinase ) inhibitor COMPOUND C in patients with Gastrointesti- nal Stromal Tumor (GIST) who failed prior therapy with imatinib and sunitinib Inclusion criteria: 1. Male or female patients 2 18 years of age 2. WHO performance status (PS) of 0-2 3. Histologically confirmed diagnosis of GIST that is unresectable or metastatic 4. ble tissue en: . Dose—escaIation cohorts: patients must have availabIe archival tumor tissue which can be shipped during the course of the study . xpansion cohort: patients must have available archival tumor tissue which can be shipped during the course of the study and must agree to a fresh pre- treatment biopsy.

. FaiIed prior therapy with imatinib followed by sunitinib for the treatment of unresectable or metastatic GIST. Note the ing specific criteria for the two phases of the trial: . Dose-escalation s: patients who failed prior therapy with imatinib and then have failed therapy with sunitinib. Treatment failure may be due to either disease progression on y (both imatinib and sunitinib) or intolerance to therapy (sunitinib).

PCT/U82012/061532 . Dose-expansion cohort: ts must have documented disease progression on both imatinib and sunitinib. In addition, patients may have had no more than two lines of prior therapy (Le. treatment with imatinib followed by treatment with sunitinib).

Claims (14)

WHAT IS CLAIMED IS:

1. Use of a c-kit inhibitor selected from the group consisting of imatinib, nilotinib and masitinib, or a pharmaceutically able salt f, respectively, and a Pl3K tor selected from the group consisting of 2-methyl-2—[4-(3—methyl-2—oxo—8—quinolin—3-yI-2,3- dihydro-imidazo[4,5-c]quinolin—1—yl)-phenyl]—propionitrile, -di-morpholin—4—yl-pyrimidin—4- yl)-4—trifluoromethyl—pyridin-2—ylamine, and (S)-pyrrolidine-1,2—dicarboxylic acid 2—amide 1- ({4-methyl[2-(2,2,2-trifluoro—1,1~dimethyl-ethyl)-pyridin-4—yl]—thiazol-2~yl}-amide), or a pharmaceutically acceptable salt thereof, respectively, in the manufacture of a medicament for the ent of gastrointestinal stromal tumors (GIST).

2. Use according to claim 1, wherein the GIST is progressing after imatinib therapy.

3. Use according to claim 1, wherein the GIST is progressing after imatinib and sunitinib therapy.

4. Use according to claim 1, wherein imatinib is adapted to be applied in a daily dose between 300 and 600 mg.

5. Use according to any one of claims 1 to 4, wherein the Pl3K inhibitor is 5-(2,6-di- morpholinyl—pyrimidin-4—yl)trifluoromethyl-pyridin—2—ylamine, or a pharmaceutically acceptable salt thereof.

6. Use according to any one of claims 1 to 4, wherein the Pl3K inhibitor is (S)—pyrrolidine-1,2— dicarboxylic acid 2—amide 1-({4-methyl[2—(2,2,2-trif|uoro-1,1-dimethy|-ethyl)—pyridin—4—yl]- thiazol-2—yl}—amide), or a pharmaceutically acceptable salt f.

7. Use according to any one of claims 1 to 4, wherein the Pl3K inhibitor is (S)-pyrrolidine-1,2— dicarboxylic acid 2-amide 1-({4-methyl[2-(2,2,2-trifluoro-1,1-dimethyl-ethyl)-pyridinyl]- thiazolyl}-amide), and the c—kit tor is imatinib, or a pharmaceutically acceptable salt thereof.

8. Combination comprising (a) a c—kit inhibitor selected from the group consisting of ib, nilotinib and masitinib, or a pharmaceutically acceptable salt thereof, respectively, and (b) a Pl3K inhibitor selected from the group consisting of 2—methyl—2—[4—(3—methyl-2—oxo-8—quinolin- 3-yI-2,3-dihydro-imidazo[4,5-c]quinoIiny|)-phenyI]-propionitri|e, -di-morpholin—4-yl— pyrimidinyl)trifluoromethyI-pyridinylamine, and (S)-pyrrolidine-1,2-dicarboxylic acid 2- amide 1-({4—methyI—5—[2-(2,2,2-trifluoro—1,1-dimethyI-ethyi)-pyridinyI]-thiazo|—2-yI}-amide), or a pharmaceutically acceptable salt thereof, respectively, adapted for the treatment of gastrointestinal stromal tumors .

9. The combination according to claim 8, wherein the GIST is progressing after imatinib therapy.

10. The combination according to claim 8, wherein the GIST is progressing after ib and sunitinib therapy.

11. The combination according to any one of claims 8 to 10, wherein the PI3K inhibitor is 5— (2,6—di-morpholin-4—yI—pyrimidin-4—yI)—4-trif|uoromethyl-pyridin—Z—yiamine, or a ceutically acceptable salt f.

12. The combination according to any one of claims 8 to 10, wherein the PI3K inhibitor is (S)- pyrrolidine-1,2-dicarboxylic acid 2—amide 1-({4-methyI[2-(2,2,2-trifiuoro-1,1-dimethyl-ethy|)- pyridinyI]-thiazol-2—yI}-amide), or a pharmaceutically acceptable salt thereof.

13. The combination according to any one of claims 8 to 10, wherein the PI3K inhibitor is (S)- pyrrolidine-1,2—dicarboxylic acid 2—amide 1-({4—methyI—5—{2-(2,2,2-trifluoro-1,1—dimethyI-ethyl)~ pyridinyI]-thiazoIyI}-amide), and the c-kit inhibitor is imatinib, or a pharmaceutically acceptable salt thereof.

14. Use according to claim 1, substantialiy as herein described with reference to any one of the Examples and/or