DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance

Targeted protein degradation (TPD) mediates protein level through small molecule induced redirection of E3 ligases to ubiquitinate neo-substrates and mark them for proteasomal degradation. TPD has recently emerged as a key modality in drug discovery. So far only a few ligases have been utilized for TPD. Interestingly, the workhorse ligase CRBN has been observed to be downregulated in settings of resistance to immunomodulatory inhibitory drugs (IMiDs). Here we show that the essential E3 ligase receptor DCAF1 can be harnessed for TPD utilizing a selective, non-covalent DCAF1 binder. We confirm that this binder can be functionalized into an efficient DCAF1-BRD9 PROTAC. Chemical and genetic rescue experiments validate specific degradation via the CRL4DCAF1 E3 ligase. Additionally, a dasatinib-based DCAF1 PROTAC successfully degrades cytosolic and membrane-bound tyrosine kinases. A potent and selective DCAF1-BTK-PROTAC (DBt-10) degrades BTK in cells with acquired resistance to CRBN-BTK-PROTACs while the DCAF1-BRD9 PROTAC (DBr-1) provides an alternative strategy to tackle intrinsic resistance to VHL-degrader, highlighting DCAF1-PROTACS as a promising strategy to overcome ligase mediated resistance in clinical settings.

BRD9 degraders as chemosensitizers in acute leukemia and multiple myeloma

Bromodomain-containing protein 9 (BRD9), an essential component of the SWI/SNF chromatin remodeling complex termed ncBAF, has been established as a therapeutic target in a subset of sarcomas and leukemias. Here, we used novel small molecule inhibitors and degraders along with RNA interference to assess the dependency on BRD9 in the context of diverse hematological malignancies, including acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and multiple myeloma (MM) model systems. Following depletion of BRD9 protein, AML cells undergo terminal differentiation, whereas apoptosis was more prominent in ALL and MM. RNA-seq analysis of acute leukemia and MM cells revealed both unique and common signaling pathways affected by BRD9 degradation, with common pathways including those associated with regulation of inflammation, cell adhesion, DNA repair and cell cycle progression. Degradation of BRD9 potentiated the effects of several chemotherapeutic agents and targeted therapies against AML, ALL, and MM. Our findings support further development of therapeutic targeting of BRD9, alone or combined with other agents, as a novel strategy for acute leukemias and MM.

Abstract 1770: A new DOT1L inhibitor with in vivo activity in mouse models of MLL-translocated leukemia

Rearrangements in the mixed lineage leukemia (MLL) gene define a distinct, aggressive form of acute leukemia with poor prognosis. The MLL gene encodes for a SET domain histone methyl transferase that catalyzes the methylation of histone 3 lysine 4 (H3K4) at specific gene loci, thus regulating transcription of developmental genes including HOX genes. In disease-linked translocations, the catalytic SET domain is lost and the remaining part fused to a variety of partners, e.g. AF4, AF9, AF10 and ENL. These MLL fusion proteins directly interact with disruptor of telomeric silencing 1-like protein (DOT1L), the only known H3K79 methyltransferase. The H3K79me2 mark is broadly associated with active transcription. Mislocated enzymatic activity of DOT1L causes local H3K79 hypermethylation, misexpression of leukomogenic genes, e.g. HOXA9 and MEIS1, and the aberrant maintenance of a stem cell-like state.

Current treatment options of MLL are limited to chemotherapy and allogeneic hematopoietic stem cell transplantation, and outcomes remain poor. The first and only clinical DOT1L inhibitor Pinometostat (EPZ-5676), an S-Adenosyl Methionine (SAM) competitive inhibitor, showed only modest activity and emerging resistance in adult acute leukemia. Pinometostat is no oral drug, but requires administration as continuous infusion to achieve sufficient exposure and sustained target inhibition. So far, there is no approved DOT1L inhibitor and the need remains to develop effective DOT1L inhibitors.

We report the identification of new SAM-competitive, structurally SAM-unrelated DOT1L inhibitors with subnanomolar biochemical potency. Compounds with nanomolar cellular activity and good exposure in mouse were tested in tumor xenograft models. Compounds 8 and 9 showed excellent blood exposure after a single dose. However, repeated dosing led to reduced exposure due to cytochrome P450 (Cyp450) 3A4 induction, insufficient pharmacodynamics (PD) and lack of efficacy. Further modification resulted in compound 10 that could be administered orally and was stable upon repeated dosing. A 300 mg/kg dose covered efficacious blood exposure for 24 h, but was not tolerated by tumor-bearing mice. Unfortunately, a 6-fold reduced dose did not achieve sufficient PD modulation and efficacy. Additional activities led to compound 11, which lost its oral bioavailability and had to be administered subcutaneously. Nevertheless, compound 11 achieved tumor growth inhibition in the MV4-11 and Molm-13 xenograft models in mice.

In conclusion, we progressed in making DOT1L inhibitors with improved PK properties, but further optimization is required to generate a viable clinical candidate. The limited efficacy obtained with compound 11 and lack of efficacy observed with subcutaneous administration of EPZ-5676 around the maximally tolerated dose illustrate the difficulty to achieve a sustained level of DOT1L inhibitor in vivo to suppress DOT1L activity sufficiently. Furthermore, H3K79me2 and efficacy in vivo seem disconnected.

Citation Format: Andreas Weiss, Frederic Stauffer, Clemens Clemens, Henrik Möbitz, Christian Ragot, Kim S. Beyer, Keith Calkins, Claudio Thoma, Daniel Guthy, Michael Kiffe, Bernard Van Eerdenbrugh, William R. Sellers, Francesco Hofmann, Ralph Tiedt, Christoph Gaul. A new DOT1L inhibitor with in vivo activity in mouse models of MLL-translocated leukemia [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1770.

New Potent DOT1L Inhibitors for in Vivo Evaluation in Mouse

In MLL-rearranged cancer cells, disruptor of telomeric silencing 1-like protein (DOT1L) is aberrantly recruited to ectopic loci leading to local hypermethylation of H3K79 and consequently misexpression of leukemogenic genes. A structure-guided optimization of a HTS hit led to the discovery of DOT1L inhibitors with subnanomolar potency, allowing testing of the therapeutic principle of DOT1L inhibition in a preclinical mouse tumor xenograft model. Compounds displaying good exposure in mouse and nanomolar inhibition of target gene expression in cells were obtained and tested in vivo.

Predictive value of cord blood bilirubin for hyperbilirubinemia in neonates at risk for maternal-fetal blood group incompatibility and hemolytic disease of the newborn

OBJECTIVE

To determine the predictive ability of cord blood bilirubin (CBB) for hyperbilirubinemia in a population at risk for maternal-fetal blood group incompatibility and hemolytic disease of the newborn.

STUDY DESIGN

This is a single center retrospective case-control study. Cases received phototherapy; controls did not. Cases were matched 1:3 to controls by gender and treating physician. Inclusion criteria included: ≥35 weeks gestation, CBB, and one or more total serum bilirubin (TSB) concentrations. The primary outcome was CBB. Secondary outcomes were a TSB >75th percentile, length of stay, and neonatal intensive care unit admission. The prognostic ability of CBB for phototherapy and TSB >75th percentile was assessed using area under the receiver operating characteristic (ROC) curve. Logistic regression analyses were performed to determine predictors for phototherapy and TSB >75th percentile.

RESULT

When compared to controls (n = 142), cases (n = 54) were more likely to have a positive Coombs' test (82% vs. 41% , p <  0.001) and TSB >75th percentile (85% vs. 21% , p <  0.001). When compared to controls, cases had a higher mean (±SD) CBB (2.5 ± 0.5 vs. 1.8 ± 0.4 mg/dL, p <  0.001). The area under the ROC curve (±SEM) for CBB for phototherapy and TSB >75th percentile was 0.87 ± 0.03 (p <  0.001, 95% CI 0.82, 0.93) and 0.87 ± 0.03 (p <  0.001, 95% CI 0.82, 0.92), respectively.

CONCLUSION

In this study, the mean CBB concentration was higher in neonates who received phototherapy compared to those who did not. CBB concentrations may help predict severe hyperbilirubinemia and phototherapy in a population at risk for hemolytic disease of the newborn.

Discovery of Novel Dot1L Inhibitors through a Structure-Based Fragmentation Approach

Oncogenic MLL fusion proteins aberrantly recruit Dot1L, a histone methyltransferase, to ectopic loci, leading to local hypermethylation of H3K79 and misexpression of HoxA genes driving MLL-rearranged leukemias. Inhibition of the methyltransferase activity of Dot1L in this setting is predicted to reverse aberrant H3K79 methylation, leading to repression of leukemogenic genes and tumor growth inhibition. In the context of our Dot1L drug discovery program, high-throughput screening led to the identification of 2, a weak Dot1L inhibitor with an unprecedented, induced pocket binding mode. A medicinal chemistry campaign, strongly guided by structure-based consideration and ligand-based morphing, enabled the discovery of 12 and 13, potent, selective, and structurally completely novel Dot1L inhibitors.

Maximizing the Efficacy of MAPK-Targeted Treatment in PTENLOF/BRAFMUT Melanoma through PI3K and IGF1R Inhibition

The introduction of MAPK pathway inhibitors paved the road for significant advancements in the treatment of BRAF-mutant (BRAF(MUT)) melanoma. However, even BRAF/MEK inhibitor combination therapy has failed to offer a curative treatment option, most likely because these pathways constitute a codependent signaling network. Concomitant PTEN loss of function (PTEN(LOF)) occurs in approximately 40% of BRAF(MUT) melanomas. In this study, we sought to identify the nodes of the PTEN/PI3K pathway that would be amenable to combined therapy with MAPK pathway inhibitors for the treatment of PTEN(LOF)/BRAF(MUT) melanoma. Large-scale compound sensitivity profiling revealed that PTEN(LOF) melanoma cell lines were sensitive to PI3Kβ inhibitors, albeit only partially. An unbiased shRNA screen (7,500 genes and 20 shRNAs/genes) across 11 cell lines in the presence of a PI3Kβ inhibitor identified an adaptive response involving the IGF1R-PI3Kα axis. Combined inhibition of the MAPK pathway, PI3Kβ, and PI3Kα or insulin-like growth factor receptor 1 (IGF1R) synergistically sustained pathway blockade, induced apoptosis, and inhibited tumor growth in PTEN(LOF)/BRAF(MUT) melanoma models. Notably, combined treatment with the IGF1R inhibitor, but not the PI3Kα inhibitor, failed to elevate glucose or insulin signaling. Taken together, our findings provide a strong rationale for testing combinations of panPI3K, PI3Kβ + IGF1R, and MAPK pathway inhibitors in PTEN(LOF)/BRAF(MUT) melanoma patients to achieve maximal response.

EXEL-7647 inhibits mutant forms of ErbB2 associated with lapatinib resistance and neoplastic transformation

PURPOSE

Mutations associated with resistance to kinase inhibition are an important mechanism of intrinsic or acquired loss of clinical efficacy for kinase-targeted therapeutics. We report the prospective discovery of ErbB2 mutations that confer resistance to the small-molecule inhibitor lapatinib.

EXPERIMENTAL DESIGN

We did in vitro screening using a randomly mutagenized ErbB2 expression library in Ba/F3 cells, which were dependent on ErbB2 activity for survival and growth.

RESULTS

Lapatinib resistance screens identified mutations at 16 different ErbB2 amino acid residues, with 12 mutated amino acids mapping to the kinase domain. Mutations conferring the greatest lapatinib resistance cluster in the NH2-terminal kinase lobe and hinge region. Structural computer modeling studies suggest that lapatinib resistance is caused by multiple mechanisms; including direct steric interference and restriction of conformational flexibility (the inactive state required for lapatinib binding is energetically unfavorable). ErbB2 T798I imparts the strongest lapatinib resistance effect and is analogous to the epidermal growth factor receptor T790M, ABL T315I, and cKIT T670I gatekeeper mutations that are associated with clinical drug resistance. ErbB2 mutants associated with lapatinib resistance transformed NIH-3T3 cells, including L755S and T733I mutations known to occur in human breast and gastric carcinomas, supporting a direct mechanism for lapatinib resistance in ErbB2-driven human cancers. The epidermal growth factor receptor/ErbB2/vascular endothelial growth factor receptor inhibitor EXEL-7647 was found to inhibit almost all lapatinib resistance-associated mutations. Furthermore, no ErbB2 mutations were found to be associated with EXEL-7647 resistance and lapatinib sensitivity.

CONCLUSIONS

Taken together, these data suggest potential target-based mechanisms of resistance to lapatinib and suggest that EXEL-7647 may be able to circumvent these effects.