AML-399: A Pan-BET Degrader Shows Broad Pre-Clinical Activity in a Large Acute Myeloid Leukemia Cohort

Abstract

Bromodomain and Extra Terminal (BET) proteins are ubiquitously expressed epigenetic “readers” that play a major role in regulating expression of oncogenic genes such as c-Myc. BET protein family are crucial for acute myeloid leukemia (AML) maintenance, and expression of BRD4 is a poor prognostic indicator in AML. We have developed novel and a highly potent proteolysis-targeting, chimera (PROTAC)-based pan-BET degrader, QCA570, that depletes BET. This BET-degrader is derived from a new class of inhibitor, HYD276. We tested QCA570 in a panel of 104 primary AML samples in ex-vivo cultures. Leukemia stem cells (LSCs) were enriched by positive selection with CD34 antibody. Cells were plated in LSC conducive medium containing growth factors and drugs for 72 hrs, and cell death and apoptosis induction was measured by flow cytometry for DAPI-Annexin V binding. Primary AML cells were obtained from newly diagnosed AML (N=89) or relapse/refractory AML (N=15). The median IC50 for BET-degrader was 120 pM, and only 13 samples had an IC50 >1 nM. In contrast, the median IC50 for the inhibitor HYD276 was 30,000 fold higher at 3.5 μM. An IC50 of greater than 10 μM HYD276 was considered as resistant to the BET inhibitor. BET inhibitor-resistant LSCs were found to be sensitive to the degrader QCA570, irrespective of mutation status and chromosomal aberrations, suggesting that there are additional mechanisms of action of the degrader as compared to the inhibitor. The AML cells were heterogeneous for the expression of mutant FLT-3 (36%), NPM1 (22%), IDH1/2 (16%), CEBP-alpha (2%), DNMT3A (2%), and other mutations (10%). Based on classical karyotype, 30% of them had a normal karyotype, and 55% had abnormal karyotype. The degradation of BRD4 and repression of c-MYC was confirmed by immunoblotting after a 4-hr exposure of LSCs to the degrader. Moreover, treatment of normal CD34-positive hematopoietic cells in an apoptosis assay and colony formation assays suggests lack of toxicity to normal hematopoiesis. Evaluation of this new class of drugs in patient-derived xenografts is ongoing. In conclusion, QCA570 represents a highly potent and efficacious pan-BET-BRD degrader undergoing extensive pre-clinical evaluation for the treatment of acute leukemias. Bromodomain and Extra Terminal (BET) proteins are ubiquitously expressed epigenetic “readers” that play a major role in regulating expression of oncogenic genes such as c-Myc. BET protein family are crucial for acute myeloid leukemia (AML) maintenance, and expression of BRD4 is a poor prognostic indicator in AML. We have developed novel and a highly potent proteolysis-targeting, chimera (PROTAC)-based pan-BET degrader, QCA570, that depletes BET. This BET-degrader is derived from a new class of inhibitor, HYD276. We tested QCA570 in a panel of 104 primary AML samples in ex-vivo cultures. Leukemia stem cells (LSCs) were enriched by positive selection with CD34 antibody. Cells were plated in LSC conducive medium containing growth factors and drugs for 72 hrs, and cell death and apoptosis induction was measured by flow cytometry for DAPI-Annexin V binding. Primary AML cells were obtained from newly diagnosed AML (N=89) or relapse/refractory AML (N=15). The median IC50 for BET-degrader was 120 pM, and only 13 samples had an IC50 >1 nM. In contrast, the median IC50 for the inhibitor HYD276 was 30,000 fold higher at 3.5 μM. An IC50 of greater than 10 μM HYD276 was considered as resistant to the BET inhibitor. BET inhibitor-resistant LSCs were found to be sensitive to the degrader QCA570, irrespective of mutation status and chromosomal aberrations, suggesting that there are additional mechanisms of action of the degrader as compared to the inhibitor. The AML cells were heterogeneous for the expression of mutant FLT-3 (36%), NPM1 (22%), IDH1/2 (16%), CEBP-alpha (2%), DNMT3A (2%), and other mutations (10%). Based on classical karyotype, 30% of them had a normal karyotype, and 55% had abnormal karyotype. The degradation of BRD4 and repression of c-MYC was confirmed by immunoblotting after a 4-hr exposure of LSCs to the degrader. Moreover, treatment of normal CD34-positive hematopoietic cells in an apoptosis assay and colony formation assays suggests lack of toxicity to normal hematopoiesis. Evaluation of this new class of drugs in patient-derived xenografts is ongoing. In conclusion, QCA570 represents a highly potent and efficacious pan-BET-BRD degrader undergoing extensive pre-clinical evaluation for the treatment of acute leukemias.