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EP-3870572-B1 - COMPOUNDS TARGETING MUTANT CALRETICULIN

EP3870572B1EP 3870572 B1EP3870572 B1EP 3870572B1EP-3870572-B1

Inventors

  • ZAGRIJTSCHUK, Oleh
  • JIA, Ruochen

Dates

Publication Date
20260506
Application Date
20191023

Claims (13)

  1. A compound selected from the group consisting of a polyheterocyclic derivative having the general formula (I) and solvates, salts, polymorphs, crystalline forms, racemic mixtures, diastereomers, enantiomers, tautomers, isotopically labeled forms, and combinations thereof, for use in a method of treating a disease or condition caused by or associated with a mutation of CALR, wherein the disease or condition is a myeloid malignancy, wherein ring Q has a formula selected from the group consisting of: and each of rings A and B is fused to ring Q and is independently selected from benzo, pyridino, pyrimidino, pyridazino, pyrazino, and hydrated forms thereof; R 1 is selected from the group consisting of H, -P(O)(OH) z (OR 85 ) 2-z , and -C(=O)R 85 , wherein R 85 is selected from the group consisting of C 1-6 alkyl, C 3-7 cycloalkyl, C 6-10 aryl, C 6-10 halogenaryl, 3- to 7-membered heterocyclyl, and 3- to 7-membered heteroaryl; and z is 0, 1, or 2; each R 2 is independently selected from the group consisting of C 1-3 alkyl, halogen, -CN, -OH, -O(C 1-3 alkyl), -NH 2 , -NH(C 1-3 alkyl), and -N(C 1-3 alkyl) 2 , or any two R 2 which are bound to the same carbon atom of ring Q may join together to form =O; each of R 3A and R 3B is independently selected from the group consisting of C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-7 cycloalkyl, C 6-10 aryl, 3- to 7-membered heterocyclyl, 3-to 7-membered heteroaryl, halogen, -CN, -NO 2 , -OH, -O(C 1-6 alkyl), -CF 3 , -OCF 3 , - O(CH 2 ) 0-2 (C 3-7 cycloalkyl), -O(CH 2 ) 0-2 (C 6-10 aryl), -O(CH 2 ) 0-2 (3- to 7-membered heteroaryl), -O(CH 2 ) 0-2 (3- to 7-membered heterocyclyl), -NH 2 , -NH(C 1-6 alkyl), -N(C 1-6 alkyl) 2 , -NHS(O) 2 (C 1-6 alkyl), -S(O) 2 NH 2-z (C 1-6 alkyl) z , -C(=O)(C 1-6 alkyl), - C(=O)OH, -OC(=O)R 11a , -C(=O)O(C 1-6 alkyl), -C(=O)NH 2-z (C 1-6 alkyl) z , -NHC(=O)H, -NHC(=O)(C 1-6 alkyl), -NHC(=NH)NH 2-z (C 1-6 alkyl) z , -N(C 1-6 alkyl)C(=NH)NH 2-z (C 1-6 alkyl) z , and -(C 1-6 alkylene)OH, wherein z is 0, 1, or 2; and R 11a is selected from the group consisting of C 1-6 alkyl, C 3-7 cycloalkyl, C 6-10 aryl, 3- to 7-membered heterocyclyl, and 3- to 7-membered heteroaryl, and is optionally substituted with one or two independently selected R 30 ; and/or any two R 3A which are bound to the same carbon atom of ring A may join together to form =O and/or any two R 3B which are bound to the same carbon atom of ring B may join together to form =O and/or any two R 3A on adjacent ring atoms of ring A may join together with the adjacent ring atoms of ring A to form a 5- to 6-membered ring which is optionally substituted with one, two or three moieties independently selected from the group consisting of -OH, methyl, ethyl, - OCH 3 , -SCH 3 , and -NH 2-z (CH 3 ) z and/or any two R 3B on adjacent ring atoms of ring B may join together with the adjacent ring atoms of ring B to form a 5- to 6-membered ring which is optionally substituted with one, two or three moieties independently selected from the group consisting of -OH, methyl, ethyl, -OCH 3 , -SCH 3 , and -NH 2-z (CH 3 ) z ; n is 0, 1, or 2, such as 0 or 2; each of m1 and m2 is independently 0, 1, 2, 3, or 4; R 30 is a 1 st level substituent selected from the group consisting of 6- to 10-membered aryl, 3- to 7-membered heteroaryl, 3- to 7-membered cycloalkyl, 3- to 7-membered heterocyclyl, - C(R 71 )=(3- to 7-membered heterocyclylidene), halogen, -CN, azido, -NO 2 , -OR 71 , -N(R 72 )(R 73 ), -S(O) 0-2 R 71 , -S(O) 1-2 OR 71 , -OS(O) 1-2 R 71 , -OS(O) 1-2 OR 71 , -S(O) 1-2 N(R 72 )(R 73 ), -OS(O) 1-2 N(R 72 )(R 73 ), -N(R 71 )S(O) 1-2 R 71 , -NR 71 S(O) 1-2 OR 71 , -NR 71 S(O) 1-2 N(R 72 )(R 73 ), -OP(O)(OR 71 ) 2 , - C(=X 1 )R 71 , -C(=X 1 )X 1 R 71 , -X 1 C(=X 1 )R 71 , and -X 1 C(=X 1 )X 1 R 71 , and/or any two R 30 which are bound to the same carbon atom of a cycloalkyl or heterocyclyl group may join together to form =X 1 , wherein each of the of 6- to 10-membered aryl, 3- to 7-membered heteroaryl, 3- to 7-membered cycloalkyl, 3- to 7-membered heterocyclyl and 3- to 7-membered heterocyclylidene groups being a 1 st level substituent is optionally substituted by one or more 2 nd level substituents, wherein said 2 nd level substituent is, in each case, independently selected from the group consisting of C 1-6 alkyl, 6-membered aryl, 5- to 7-membered heteroaryl, 5- to 7-membered cycloalkyl, 5- to 7-membered heterocyclyl, halogen, -CF 3 , -CN, azido, -NO 2 , -OH, and -NH 2 , and/or any two 2 nd level substituents which are bound to the same carbon atom of a cycloalkyl or heterocyclyl group being a 1 st level substituent may join together to form =O or =S and/or any two 2 nd level substituents which are bound to the same carbon atom of a cycloalkyl or heterocyclyl group being a 1 st level substituent may join together to form =C(R 81 )(6- to 14-membered aryl) or =C(R 81 )(3- to 14-membered heteroaryl), wherein each of the C 1-6 alkyl, 6-membered aryl, 6- to 14-membered aryl from the =C(R 81 )(6- to 14-membered aryl) group, 5- to 7-membered heteroaryl, 3- to 14-membered heteroaryl from the =C(R 81 )(3- to 14-membered heteroaryl) group, 5- to 7-membered cycloalkyl, 5- to 7-membered heterocyclyl groups being a 2 nd level substituent is optionally substituted with one or more 3 rd level substituents, wherein said 3 rd level substituent is, in each case, independently selected from the group consisting of C 1-3 alkyl, halogen, -CF 3 , -CN, azido, -NO 2 , -OH, -O(C 1-3 alkyl), -OCF 3 , -S(C 1-3 alkyl), -NH 2 , - NH(C 1-3 alkyl), -N(C 1-3 alkyl) 2 , -NHS(O) 2 (C 1-3 alkyl), -S(O) 2 NH 2-z (C 1-3 alkyl) z , -C(=O)OH, - C(=O)O(C 1-3 alkyl), -C(=O)NH 2-z (C 1-3 alkyl) z , -NHC(=O)(C 1-3 alkyl), -NHC(=NH)NH 2-z (C 1-3 alkyl) z , and -N(C 1-3 alkyl)C(=NH)NH 2-z (C 1-3 alkyl) z , wherein z is 0, 1, or 2 and C 1-3 alkyl is methyl, ethyl, propyl or isopropyl, and/or any two 3 rd level substituents which are bound to the same carbon atom of a 5- to 7-membered cycloalkyl or heterocyclyl group being a 2 nd level substituent may join together to form =O, =S, or =NH; wherein R 71 , R 72 , and R 73 are independently selected from the group consisting of H, C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, 3- to 7-membered cycloalkyl, 5- or 6-membered aryl, 5- or 6-membered heteroaryl, and 3- to 7-membered heterocyclyl, wherein each of the C 1-6 alkyl, C 2-6 alkenyl, C 2-6 alkynyl, 3- to 7-membered cycloalkyl, 5- or 6-membered aryl, 5- or 6-membered heteroaryl, and 3- to 7-membered heterocyclyl groups is optionally substituted with one, two or three substituents selected from the group consisting of C 1-3 alkyl, halogen, -CF 3 , -CN, azido, -NO 2 , -OH, -O(C 1-3 alkyl), -OCF 3 , =O, -S(C 1-3 alkyl), -NH 2 , -NH(C 1-3 alkyl), -N(C 1-3 alkyl) 2 , -NHS(O) 2 (C 1-3 alkyl), -S(O) 2 NH 2-z (C 1-3 alkyl) z , -C(=O)(C 1-3 alkyl), -C(=O)OH, -C(=O)O(C 1-3 alkyl), -C(=O)NH 2-z (C 1-3 alkyl) z , - NHC(=O)(C 1-3 alkyl), -NHC(=NH)NH 2-z (C 1-3 alkyl) z , and -N(C 1-3 alkyl)C(=NH)NH 2-z (C 1-3 alkyl) z , wherein z is 0, 1, or 2 and C 1-3 alkyl is methyl, ethyl, propyl or isopropyl; R 81 is independently selected from the group consisting of H, C 1-4 alkyl, C 2-4 alkenyl, C 2-4 alkynyl, 3- to 6-membered cycloalkyl, 5- or 6-membered aryl, 5- or 6-membered heteroaryl, and 3- to 6-membered heterocyclyl, wherein each of the C 1-4 alkyl, C 2-4 alkenyl, C 2-4 alkynyl, 3- to 6-membered cycloalkyl, 5- or 6-membered aryl, 5- or 6-membered heteroaryl, and 3- to 6-membered heterocyclyl groups is optionally substituted with one, two or three substituents selected from the group consisting of C 1-3 alkyl, halogen, -CF 3 , -CN, azido, -NO 2 , -OH, -O(C 1-3 alkyl), -OCF 3 , =O, -S(C 1-3 alkyl), -NH 2 , -NH(C 1-3 alkyl), -N(C 1-3 alkyl) 2 , -NHS(O) 2 (C 13 alkyl), -S(O) 2 NH 2-z (C 1-3 alkyl) z , -C(=O)(C 1-3 alkyl), -C(=O)OH, -C(=O)O(C 1-3 alkyl), -C(=O)NH 2-z (C 1-3 alkyl) z , - NHC(=O)(C 1-3 alkyl), -NHC(=NH)NH 2-z (C 1-3 alkyl) z , and -N(C 1-3 alkyl)C(=NH)NH 2-z (C 1-3 alkyl) z , wherein z is 0, 1, or 2 and C 1-3 alkyl is methyl, ethyl, propyl or isopropyl; and X 1 and X 2 are independently selected from O, S, and N(R 84 ), wherein R 84 is -H or C 1-3 alkyl.
  2. The compound for use of claim 1, wherein ring Q (a) has a formula selected from the group consisting of: (b) has a formula selected from the group consisting of: or (c) has a formula selected from the group consisting of:
  3. The compound for use of any one of claims 1 to 2, wherein each of rings A and B is independently selected from benzo, pyridino, pyrimidino, and hydrated forms thereof, wherein the sum of m1 and m2 is 1 to 7, preferably the sum of m1 and m2 is 1, 2, 3, 4, 5, or 6.
  4. The compound for use of any one of claims 1 to 3 having one of the following formulas:
  5. The compound for use of any one of claims 1 to 4, wherein each of R 3A and R 3B is independently selected from the group consisting of C 1-4 alkyl, halogen, -CN, -NO 2 , -OH, -O(C 1-3 alkyl), -O(CH 2 ) 1-2 (C 3-7 cycloalkyl), -O(CH 2 ) 1-2 (C 6-10 aryl), -O(CH 2 ) 1-2 (3- to 7-membered heteroaryl), -O(CH 2 ) 1-2 (3- to 7-membered heterocyclyl), -NH 2 , -NH(C 1-3 alkyl), -N(C 1-3 alkyl) 2 , -OC(=O)(R 11a ), -C(-O)NH 2-z (C 1-6 alkyl) z , -NHC(=O)H, -NHC(=O)(C 1-6 alkyl), and -(C 1-3 alkylene)OH, wherein z is 0, 1, or 2; and R 11a is selected from the group consisting of C 1-3 alkyl and phenyl, each of which is optionally substituted with one or two independently selected R 30 ; and/or any two R 3A which are bound to the same carbon atom of ring A may join together to form =O and/or any two R 3B which are bound to the same carbon atom of ring B may join together to form =O and/or any two R 3A on adjacent ring atoms of ring A may join together with the adjacent ring atoms of ring A to form a 5- to 6-membered heterocyclyl which is optionally substituted with one, two or three moieties independently selected from the group consisting of -OH, methyl, ethyl, -OCH 3 , and -NH 2-z (CH 3 ) z and/or any two R 3B on adjacent ring atoms of ring B may join together with the adjacent ring atoms of ring B to form a 5- to 6-membered heterocyclyl which is optionally substituted with one, two or three moieties independently selected from the group consisting of -OH, methyl, ethyl, -OCH 3 , and -NH 2-z (CH 3 ) z .
  6. The compound for use of any one of claims 1 to 5, wherein R 1 is selected from the group consisting of H, -C(=O)(C 6 halogenaryl), and -C(=O)(C 1-3 alkyl).
  7. The compound for use of any one of claims 1 to 6, wherein the myeloid malignancy is a myeloproliferative neoplasm or a myelodysplasia syndrome, wherein the myeloproliferative neoplasm is preferably selected from the group consisting of prefibrotic myelofibrosis (pre-PMF), primary myelofibrosis (PMF) and essential thrombocythemia (ET); and/or the myelodysplastic syndrome preferably is refractory anemia with ringed sideroblasts and thrombocythemia (RARS-T).
  8. The compound for use of any one of claims 1 to 7, wherein the compound is selected from the group consisting of: and solvates, salts, polymorphs, crystalline forms, racemic mixtures, diastereomers, enantiomers, tautomers, and isotopically labeled forms thereof.
  9. Use of a compound as defined in any one of claims 1 to 8 in a method of screening for compounds that selectively inhibit growth of CALR mutant cells and/or exhibit selective cytotoxicity towards CALR mutant cells, wherein the compound as defined in any one of claims 1 to 8 is used as a reference compound.
  10. Method of screening for compounds that are suitable for treating a disease or condition caused by or associated with a mutation of CALR, wherein the disease or condition is a myeloid malignancy, said method comprising the steps: (a) providing a compound; (b) testing the compound for binding to one or more glycan-, Ca 2+ - and/or ATP-binding sites of calreticulin, and (c) testing the compound for selective inhibition of growth of CALR mutant cells and/or selective cytotoxicity towards CALR mutant cells, wherein a compound that (i) binds to one or more glycan-, Ca 2+ - and/or ATP-binding sites of calreticulin and (ii) selectively inhibits growth of CALR mutant cells and/or exhibits selective cytotoxicity towards CALR mutant cells is identified as a compound that is suitable for treating a disease or condition caused by or associated with a mutation of CALR, wherein a compound as defined in any one of claims 1 to 8 is used as a reference compound.
  11. The method of claim 10, wherein the compound is tested for binding to the N-glycan binding site of calreticulin.
  12. The method of claim 10 or 11, wherein step (b) is performed in silico.
  13. The method of any one of claims 10 to 12, wherein the myeloid malignancy is a myeloproliferative neoplasm or a myelodysplasia syndrome, wherein the myeloproliferative neoplasm is preferably selected from the group consisting of prefibrotic myelofibrosis (pre-PMF), primary myelofibrosis (PMF) and essential thrombocythemia (ET); and/or the myelodysplastic syndrome preferably is refractory anemia with ringed sideroblasts and thrombocythemia (RARS-T).

Description

TECHNICAL FIELD OF THE INVENTION The present invention relates to compounds binding to calreticulin which selectively inhibit growth of CALR mutant cells and/or exhibit selective cytotoxicity towards CALR mutant cells, to pharmaceutical compositions comprising such compounds as well as to their use in treating diseases or conditions caused by or associated with a mutation of CALR, in particular myeloid malignancies, such as myeloproliferative neoplasms or myelodysplasia syndrome. The present invention also relates to screening assays allowing the identification of such compounds. TECHNICAL BACKGROUND OF THE INVENTION The classical myeloproliferative neoplasms (MPN) are clonal hematopoietic diseases which are driven by somatic mutations acquired by hematopoietic stem/progenitor cells. Three phenotypic driver mutations have been identified in MPN which include mutations in the JAK2, c-MPL and CALR genes, which all result in constitutive activation of the Janus kinase (JAK)/signal transducers and activators of transcription (STAT) pathway (Baxter EJ et al., Lancet, 2005, 365(9464):1054-61; James C et al., Nature, 2005, 434(7037):1144-8; Kralovics R et al., N Engl J Med., 2005, 352(17):1779-90; Levine RL et al., Cancer Cell, 2005, 7(4):387-97; Scott LM et al., N Engl J Med., 2007, 356(5):459-68; Pikman Y et al., PLoS Med, 2006, 3(7):e270; Klampfl T et al., N Engl J Med., 2013, 369(25):2379-90; Nangalia J et al., N Engl J Med., 2013, 369(25):2391-405). Calreticulin mutations occur at exon 9 of the CALR gene, leading to an alternative reading frame protein product at the C-terminus which eliminates most of the original negatively charged amino acids as well as the KDEL ER retention sequence and replaces them with positively charged sequences enriched with lysine and arginine residues. Deletion 52bp (CALR del52) is the most frequent mutation which contributes to more than 50% of mutant CALR cases, followed by insertion 5bp (CALR ins5) which accounts for over 30% of the cases (Klampfl T et al., N Engl J Med., 2013, 369(25):2379-90; Nangalia J et al., N Engl J Med., 2013, 369(25):2391-405). Pathogenesis of mutant calreticulin has been investigated extensively since its discovery, and major progress has been made by a few research groups. The requirement of thrombopoietin receptor (MPL) in the oncogenic function of mutant calreticulin has been revealed in CALR mutant cell line models. For instance, cytokine independent growth of BalF3, UT-7 and 32D cells can be induced by CALR mutations only if MPL is expressed either endogenously or ectopically in these cell lines and the outgrowth is accompanied by the constitutive activation of downstream JAK-STAT pathways (Araki M et al., Blood, 2016, 127(10):1307-16; Chachoua I et al., Blood, 2016, 127(10):1325-35; Elf S et al., Cancer Discov., 2016, 6(4):368-81; Han L et al., J Hematol Oncol., 2016, 9(1):45; Marty C et al., Blood, 2016, 127(10):1317-24; Nivarthi H et al., Leukemia, 2016, 30(8):1759-63). Transgenic mice models carrying CALR disease frameshift mutations develop essential thrombocythemia phenotype characterized by elevation of platelets count and increased number of megakaryocytes in the bone marrow (Marty C et al., Blood, 2016, 127(10):1317-24; Li J et al., Blood, 2018, 131(6):649-61; Shide K et al., Leukemia, 2017, 31(5):1136-44). Physical interactions between mutant calreticulin and MPL have also been detected by co-immunoprecipitation, and the novel C-terminal peptide generated by the mutation is essential to this interaction (Araki M et al., Blood, 2016, 127(10):1307-16; Elf S et al., Blood, 2018, 131(7):782-6). Further studies suggest that mutant calreticulins tend to form oligomers and might interact with MPL as a homomultimeric complex (Araki M et al., Leukemia, 2018, published online on June 26). On the other hand, the calreticulin-MPL interaction seems crucial but not sufficient for the activation of downstream oncogenic pathways, as the truncation of the last 36 amino acids at the mutant protein C-terminus abolishes its oncogenic activity but retains the interaction with MPL (Elf S et al., Blood, 2018, 131(7):782-6). An important domain for mutant calreticulin to activate the downstream oncogenic pathway is the N-glycan binding domain/site located in the globular lectin part of the protein. This domain mediates the binding of N-glycosylated protein substrates with calreticulin in the endoplasmic reticulum lumen, as part of calreticulin's chaperone function facilitating proper protein folding (Peterson JR et al., Mol Biol Cell., 1995, 6(9):1173-84). Mutagenesis at the two amino acid residues which has been shown to abrogate glycan binding capacity of calreticulin also abolishes JAK-STAT pathway activation by mutant calreticulin (Chachoua I et al., Blood, 2016, 127(10):1325-35; Kapoor M et al., Biochemistry, 2004, 43(1):97-106). Also, as MPL is a glycosylated protein, it has been shown that MPL activates mutant calreticulin through its glycosylation sites