ALK2 Inhibitors Research Articles

DIPG-22. A NOVEL ROLE FOR ACVR1/ALK2 IN REGULATING CHOLESTEROL BIOSYNTHESIS PROVIDES A NEW COMBINATORIAL THERAPEUTIC APPROACH FOR PATIENTS WITH DMG

Abstract BACKGROUND The discovery of somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, in 20-25% of diffuse midline glioma H3K27-altered (DMG-H3K27) patients has led to the development of numerous chemotypes of ALK2 inhibitor (ALK2i). However, in models of ACVR1-mutant DMG-H3K27 the efficacy of single-agent ALK2i’s has been modest and new combinatorial treatment approaches are desperately needed. METHODS We performed unbiased combinatorial genetic and drug screens in patient-derived ACVR1-mutant DMG-H3K27 cells in vitro, using multiple chemotypes of ALK2i. We also generated in vitro transcriptomic, proteomic and metabolomic profiles of three ACVR1-mutant DMG-H3K27 models following ALK2i treatment. RESULTS The top ALK2i sensitising CRISPR hits (vehicle vs. ALK2i) were analysed using gene set enrichment analysis (GSEA) which revealed specific genetic dependencies in cholesterol synthesis/regulation following both M4K2009 and TP-0184 treatment. The top CRISPR hits included multiple key nodes of cholesterol biosynthesis such as HMGCR (HMG-CoA>mevalonate), LSS (squalene-2-2-epoxide>lanosterol) and DHCR24 (lanosterol>cholesterol). These hits were pharmacologically mirrored in the top hits identified from the drug screen, including drugs that either directly or indirectly target cholesterol synthesis. Integration of the multi-omic data revealed a raft of changes associated with cholesterol biosynthesis/efflux. The expression of HMGCR/HMGCS1 (cholesterol synthesis) and LXR/ABCA1 (cholesterol export) were down and upregulated, respectively, with metabolomic data showing a reduction in cholesterol and it’s derivative 4-cholesten-3-one and an increase in desmosterol, an immediate precursor to cholesterol synthesis. Highly synergistic interactions were observed between multiple ALK2i and a panel of pharmacological agents targeting the cholesterol synthesis/efflux pathway, including routinely used drugs such as simvastatin and lovastatin, clinically well-tolerated and with good CNS penetrance in immuno-compromised and immune-competent mouse models, in whom in vivo combination studies are ongoing. CONCLUSIONS These data provide evidence for a previously unappreciated link between ALK2 signalling and metabolism, and identify readily translatable combination partners for ALK2i in the clinic.

Discovery of Conformationally Constrained ALK2 Inhibitors.

Despite decades of research on new diffuse intrinsic pontine glioma (DIPG) treatments, little or no progress has been made on improving patient outcomes. In this work, we explored novel scaffold modifications of M4K2009, a 3,5-diphenylpyridine ALK2 inhibitor previously reported by our group. Here we disclose the design, synthesis, and evaluation of a first-in-class set of 5- to 7-membered ether-linked and 7-membered amine-linked constrained inhibitors of ALK2. This rigidification strategy led us to the discovery of the ether-linked inhibitors M4K2308 and M4K2281 and the amine-linked inhibitors M4K2304 and M4K2306, each with superior potency against ALK2. Notably, M4K2304 and M4K2306 exhibit exceptional selectivity for ALK2 over ALK5, surpassing the reference compound. Preliminary studies on their in vivo pharmacokinetics, including blood-brain barrier penetration, revealed that these constrained scaffolds have favorable exposure and do open a novel chemical space for further optimization and future evaluation in orthotopic models of DIPG.

ALK2 and JAK2 Inhibition for Improved Treatment of Anemia in Myelofibrosis Patients: Preclinical Profile of an ALK2 Inhibitor Zilurgisertib in Combination with Ruxolitinib

Introduction: Anemia is a common occurrence in patients with myelofibrosis (MF) and is associated with the need for red blood cell transfusion and poor clinical prognosis. JAK inhibitors such as ruxolitinib are used extensively to treat symptoms of MF and improve quality of life and overall survival. However, JAK inhibitors may also contribute to myelosuppression. Therapeutic interventions that allow for optimization of JAK inhibition with no concern of anemia would benefit patients with MF and potentially lower the rate of treatment discontinuation or suboptimal dosing. Recent studies have demonstrated that inhibition of ACVR1/ALK2, a bone morphogenetic protein receptor that is upstream of the transcriptional regulation of hepcidin, could reduce serum hepcidin levels in patients with MF and improve anemia (Verstovsek S et al. Lancet 2023; Oh S et al. Clin Lymphoma Myeloma Leuk 2022). Reducing levels of hepcidin, a key regulator of plasma iron levels, and restoring erythropoiesis would broadly benefit patients with MF. Based on these recent data, we developed zilurgisertib, a potent and selective ALK2 inhibitor that could be administered in combination with ruxolitinib at doses titrated to the needs of patients with MF. Methods and Results: In biochemical and cellular assays, zilurgisertib inhibited ALK2 kinase activity and SMAD1/5 phosphorylation with IC 50 values of 15 nM and 63 nM, respectively. In Huh-7 cells stimulated with BMP-6, zilurgisertib inhibited hepcidin production with an IC 50 of 20 nM, demonstrating the compound is a potent ALK2 inhibitor capable of regulating iron homeostasis via hepcidin. To assess possible off-target effects of zilurgisertib, kinome profiling at 10 μM ATP was performed at Reaction Biology (Malvern, PA) to determine the overall specificity across 356 kinases (see Figure). At 200 nM, zilurgisertib only inhibited ALK2, ALK1 (to 50%), and ALK6 (to 48%). In addition, zilurgisertib at 20 μM did not affect viability of HEK293 cells, a human cell line commonly used to assess general cell health and compound toxicity. Similarly, zilurgisertib did not affect viability of human fibroblasts or endothelial cells at concentrations up to 5 μM. To test whether the combination of ruxolitinib and zilurgisertib could suppress hepcidin and restore erythropoiesis in an in vivo mouse model of cancer-induced anemia, B16F10 cells were injected intraperitoneally, mimicking a metastatic tumor that leads to anemia 1 week after injection. In a dose-dependent manner, zilurgisertib improved hemoglobin by 2 to 3 g/dL and red blood cell counts, while reducing both liver pSMAD and circulating hepcidin levels by 50% or more compared with vehicle control. The combination of zilurgisertib with ruxolitinib had no effect on this activity, suggesting that inhibition of JAK2 does not inhibit erythropoiesis restored following ALK2 inhibition. Conclusion: Taken together, the potent and selective on-target activity of zilurgisertib suggests that ALK2 inhibition could reduce hepcidin and improve anemia, and that the combination of zilurgisertib with ruxolitinib is a rational and attractive approach to mitigate anemia in patients with MF. The combination of ruxolitinib and zilurgisertib is currently being evaluated in a phase 1 clinical trial in patients with anemia due to myeloproliferative disorders (NCT04455841).

DIPG-29. A CONNECT CONSORTIUM PRECLINICAL STUDY IDENTIFIES MEK INHIBITION AND RADIATION AS POTENTIAL COMBINATION PARTNERS FOR THE ALK2 INHIBITOR TP-0184 IN ACVR1-MUTANT DMG

Abstract Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant orthotopic xenografts with multiple chemotypes of ALK2 inhibitors (ALK2i) results in extended survival in vivo but, as single agents, these inhibitors are unable to achieve a complete anti-tumour response. To identify novel combination strategies alongside ALK2 inhibition, five international laboratories pooled resources to evaluate the ALK2i TP-0184 across 26 patient-derived DMG-H3K27 models in vitro, demonstrating GI50 values of ~0.5-10uM, although with no significant difference between ACVR1-mutant and wild-type. Genome-scale CRISPR screens of ALK2i-treated ACVR1-mutant models revealed specific genetic dependencies in critical nodes of several signalling pathways including MTOR, as well as PPP2R1A, known to play a role in MAPK pathway activation. Biomarker analysis showed inhibition of phospho-SMAD1/5/9 by western blot, with RNAseq and proteomic analysis indicating downstream signalling consequences in BMP/SMAD signalling following TP-0184 treatment. We observed synergistic pharmacological interactions between TP-0184 and both everolimus (mTORi) and trametinib (MEKi) in 7 to 8 ACVR1-mutant DMG models, respectively, with the latter validated across laboratories using orthogonal assays. Importantly, combining TP-0184 with radiation in vitro showed a profound radiosensitisation effect of the ALK2i in three ACVR1-mutant models using both clonogenic and cell viability assays in multiple laboratories, in part due to an observed activation of phospho-SMAD1/5/9 by radiation. Finally, in vivo tolerability and pharmacokinetic assays in multiple immuno-compromised and immune-competent mouse strains suggested a dose of 150mg/kg TP-0184 and 0.4mg/kg trametinib for use in in vivo efficacy studies, with good CNS penetrance of both drugs in excess of in vitro GI50 values. Such studies have been initiated in six DMG-H3K27 models across our laboratories to robustly assess the combination of TP-0184 and trametinib/radiation to support rapid potential translation to clinical trial.

Phase 1/2 study of the activin receptor-like kinase (ALK)-2 inhibitor zilurgisertib (INCB000928, LIMBER-104) as monotherapy or with ruxolitinib (RUX) in patients (pts) with anemia due to myelofibrosis (MF).

7017 Background: Elevated levels of the iron regulator hepcidin can cause functional iron deficiency anemia; hepcidin dysregulation is central to anemia of chronic inflammation observed in several malignancies such as MF. ALK2 (ie, ACVR1) contributes to MF-associated anemia via hepcidin upregulation. We evaluated the safety and activity of zilurgisertib, a selective, oral ALK2 inhibitor, in pts with anemia due to MF. Methods: The ongoing open-label, multicenter, phase 1/2 dose-escalation/expansion INCB 00928-104 study (NCT04455841) is evaluating zilurgisertib alone (treatment group A [TGA]) or with RUX (treatment group B [TGB]). Eligible pts are ≥18 years old with primary/secondary MF of intermediate (Int)-1 (TGB only) or Int-2/high-risk (TGA and TGB) per the Dynamic International Prognostic Scoring System (DIPSS) and are transfusion-dependent or have symptomatic anemia. The primary endpoint is safety and tolerability. Secondary endpoints include efficacy (per anemia response parameters), pharmacokinetics, and pharmacodynamics (eg, hepcidin and iron metabolism parameters). Results: 31 pts were enrolled by data cutoff (30Nov2022), with 20 in TGA (50 mg once daily [qd], n = 4; 100 mg qd, n = 4; 200 mg qd, n = 6; 400 mg qd, n = 6) and 11 in TGB (100 mg qd, n = 4; 200 mg qd, n = 5; 400 mg qd, n = 2). Median (range) age was 73 (53–84) y for TGA and 77 (64–85) y for TGB. 65% of TGA pts had received prior RUX therapy. Overall, 90% of pts had Int-2 risk DIPSS, and the remainder had high-risk DIPSS (1 pt in TGA, 2 in TGB). 60% of pts in TGA and 27% in TGB were transfusion-dependent at the time of enrollment. Median baseline (BL) hemoglobin (Hb) was 7.7 (range, 7–10) g/dL in TGA and 8.5 (range, 8–9) g/dL in TGB. BL hepcidin was high in both cohorts (median [range]: TGA, 171 [18–535] ng/mL; TGB, 123 [7–250] ng/mL; normal range, 0–50 ng/mL). At the time of analysis, dose escalation was ongoing in both treatment groups. No dose-limiting toxicities (DLTs) or study drug–related serious adverse events (AEs) occurred in either treatment group. Maximum tolerated dose had not been reached at the time of analysis. Treatment-emergent AEs (TEAEs) were mainly low grade. Grade ≥3 TEAEs occurred in 7 pts, with thrombocytopenia the most common (n = 4). Reduction in hepcidin following zilurgisertib dosing was observed in TGA and TGB, with maximal hepcidin reduction at 6 h postdose. Hb increase of > 1.5 g/dL from BL occurred in 3 pts (27%) in TGB and 1 pt (5%) in TGA. Conclusions: Treatment with zilurgisertib monotherapy or in combination with RUX in this patient population was generally well tolerated, with predominantly grade 1/2 TEAEs and no DLTs. Reduced hepcidin levels were observed with both monotherapy and in combination with RUX, and preliminary improvements in anemia were observed, which suggest potential for therapeutic activity. Clinical trial information: NCT04455841 .

Abstract CT243: Clinical trial simulation to inform dose selection of zilurgisertib, an ALK2 inhibitor, in patients with anemia due to myelofibrosis (MF)

Abstract Disease-associated anemia is reported in over one-third of patients at MF diagnosis and can be exacerbated by currently available MF therapies. Further, anemia is associated with poor prognosis in MF. Activation of activin receptor-like kinase (ALK)-2 (also known as ACVR1) may contribute to MF-associated anemia via up-regulated levels of hepcidin. Zilurgisertib (INCB000928) is a potent and selective ALK2 inhibitor that has demonstrated dose-dependent improvement in hemoglobin levels in a cancer-induced anemia mouse model, in which maximum hemoglobin increase was observed when zilurgisertib trough concentration covered pSMAD IC50 for at least half of the dosing interval. Zilurgisertib is being evaluated as monotherapy or in combination with ruxolitinib in a phase 1/2 dose-escalation and -expansion study in patients with anemia due to MF (NCT04455841). The objective of the current study is to use modeling and simulation, which integrate both preclinical and clinical data, to inform dose finding for the ongoing phase 1/2 trial in MF patients. Population (Pop) PK analyses were conducted using a total of 3089 zilurgisertib plasma concentrations from 161 healthy subjects in 3 completed phase 1 studies: a single ascending dose study (64 subjects, 10-500 mg), a multiple ascending dose study (59 subjects, 50-400 mg QD and 300 mg BID), and a drug-drug interaction study (38 subjects, 100 mg single dose of zilurgisertib alone). A nonlinear mixed-effects modeling approach in Monolix software was used for the analyses. Zilurgisertib PK were well-characterized by a 3-compartment model with nonlinear clearance and inter-occasion variability on absorption rate constant and bioavailability. The diagnostic plots and visual predictive check demonstrated that the model appropriately characterized the zilurgisertib plasma concentrations. Because zilurgisertib PK are similar between MF patients and healthy subjects, as suggested by available PK data in MF patients receiving doses up to 200 mg, the pop PK model developed with data from healthy subjects was used to simulate steady-state exposures in MF patients receiving 200 to 600 mg daily dose. Simulation results showed that daily doses of ≥600 mg would result in >90% of patients achieving exposure similar to the observed exposure associated with maximum efficacy in the mouse model. The conclusions from this clinical trial simulation support the decision to continue dose escalation in MF patients receiving zilurgisertib monotherapy. Citation Format: Yan-ou Yang, Hong Yang, Betty Lamothe, Matthew Stubbs, Amanda McBride, Francis Seguy, Kevin Rockich, Jay Getsy, Phillip Wang, Xiang Liu, Jeff Jackson, Ekaterine Asatiani, Xuejun Chen. Clinical trial simulation to inform dose selection of zilurgisertib, an ALK2 inhibitor, in patients with anemia due to myelofibrosis (MF) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT243.

Preliminary Results of a Phase-2 Clinical Trial of the ALK-2 Inhibitor Ker-047 for Treatment of Iron Refractory Iron Deficiency Anemia

Background: Iron refractory iron deficiency anemia (IRIDA) is a rare autosomal recessive disorder, caused by a genetic defect in TMPRSS6. This results in increased signaling through the bone morphogenic protein (BMP)/sons of mothers against decapentaplegic (SMAD) pathway, leading to disproportionally high levels of hepcidin relative to body iron status. Hepcidin reduces iron transport to the plasma by degrading the cellular iron exporter ferroportin, resulting in systemic iron deficiency and microcytic anemia. Symptomatic interventions such as intravenous iron administration results in iron sequestration in the reticular endothelial system (RES) and generally only a partial response of hemoglobin concentrations. Further, the potential long-term adverse effects of chronic intravenous iron therapy and associated elevated RES-iron levels are unknown in these patients. Blood transfusion can be administered in cases of severe symptomatic anemia but is generally avoided due to transfusion-related risks. Currently, there is an unmet need for more effective, safe, convenient, and direct-acting treatments for IRIDA. Given the central role of aberrant BMP/SMAD signaling in hepcidin production, selective inhibition of the BMP receptor ALK2 to reduce hepcidin represents a rational approach to target a precipitating factor of IRIDA. Preclinical studies in the TMPRSS6 siRNA knockdown mouse model of IRIDA demonstrated that treatment with a selective ALK2 inhibitor reduced hepcidin, increased serum iron, and ameliorated anemia. KER-047 is a novel, oral, investigational, small-molecule kinase inhibitor with potent and selective inhibitory activity against the ALK2 receptor. In a Phase 1 clinical trial, single-ascending and multiple-ascending doses of KER-047 administered to healthy participants resulted in robust decreases from baseline in hepcidin levels, increases in serum iron and transferrin saturation (TSAT), decreases in serum ferritin, and increases in reticulocyte hemoglobin content (Ret-He). Based on these observations, KER-047 was advanced to Phase 2 clinical trials. Aims: The primary objective of this ongoing Phase 2 clinical trial is to evaluate the safety and tolerability of ascending doses of KER-047 in participants with IRIDA. Secondary objectives include evaluation of pharmacokinetic (PK) and pharmacodynamic (PD) parameters. Methods: This is a 2-part open label, dose escalation and dose expansion trial. Part 1 (dose escalation) consists of up to 4 ascending dose cohorts starting with 25 mg q.d. Part 2 will be the dose expansion phase with safety as the primary focus. Patients diagnosed with IRIDA may enroll in all cohorts in Parts 1 and 2. Key inclusion criteria include diagnosis of IRIDA based on a homozygous or compound heterozygous TMPRSS6 genotype, a TSAT <15%, a ferritin level 50-700 µg/L and hemoglobin <13.8 g/dL (males) or <12.7g/dL (females) and signed informed consent. Patients are excluded if they have received IV iron treatment within 28 days prior to trial entry. Participants will be treated once daily with KER-047 for a 2-week period, followed by a 2-week washout period. Data are analyzed by using descriptive statistics. Results: At the time of this abstract submission, one participant had enrolled in the first dose-expansion cohort (KER-047 25mg q.d.). This participant reported intermittent dizziness, however no serious adverse events were observed during treatment. Hemoglobin concentration and mean corpuscular volume remained stable. Ret-He increased by day 5 of treatment. Ferritin levels decreased during treatment and returned to baseline levels after the 2-week treatment period. TSAT/hepcidin ratio, which is characteristically below reference intervals in IRIDA patients, was slightly increased but returned to baseline levels after 2-weeks treatment. Conclusion: Data are preliminary and limited to a single participant thus far in whom KER-047 25mg q.d. was well tolerated. Changes in red cell and iron parameters at this low dose support development of KER-047 as an agent to potentially address an underlying cause of IRIDA. At the time of this abstract submission, two additional patients are scheduled for screening to complete the first dose cohort. We anticipate data from the total of three patients in time for the presentation to further characterize safety of KER-047 and substantiate effects on iron metabolism. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

EXTH-41. COMBINED PHARMACOLOGICAL AND GENETIC SCREENING TO IDENTIFY DEPENDENCIES AND COMBINATIONS IN ACVR1-MUTANT DIFFUSE MIDLINE GLIOMA

Abstract Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant patient-derived models with multiple chemotypes of ALK2 inhibitors (ALK2i) results in reduced cell viability in vitro and extended survival in orthotopic xenografts in vivo but, as single agents, these inhibitors were unable to achieve a complete anti-tumour response. Recently we reported that combinatorial treatment of ACVR1-mutant DIPG cells with vandetanib (RTK inhibitor) and everolimus (mTOR/ABC transporter inhibitor) was synergistic both in vitro and in vivo and was shown to be a feasible combination to trial clinically in this setting. To identify specific dependencies in ACVR1-mutant cells which may be translatable with novel synergistic drug combinations alongside ALK2i, we have implemented both candidate and unbiased drug and genetic screening approaches. Using a panel of 13 patient-derived ACVR1-mutant models (and 6 wild-type controls), we identified synergy between multiple chemotypes of ALK2i (M4K2009/LDN-214117) and PI3K/mTOR (AZD8055/everolimus) and MEK inhibitors (trametinib), reflecting the common co-segregation of PIK3CA/PIK3R1 alterations in these tumours. Whole-genome CRISPR/Cas9 screening of ACVR1-mutant SU-DIPG-IV cells in combination with two ALK2i (M4K2009/LDN-193189), confirmed a specific MTOR genetic dependency, as well as for the protein phosphatase regulatory subunit PPP2R1A, known to play a role in MAPK pathway activation. Additional hits include the serine/threonine kinase PKMYT1, a negative regulator of the G2/M checkpoint via a functionally redundant phosphorylation of CDK1/CCNB1 alongside WEE1; confirmatory drug assays with the WEE1 inhibitor AZD1775 resulted in a synergistic interaction with ALK2i in ACVR1-mutant cells. Hits were integrated with DepMap using ‘gene effect’ scores (Chronos) enabling filtering of common essential genes. Preliminary pathway enrichment analysis (MAGeCKFlute) identified ALK2i-specific vulnerabilities involving TGFB1/SMAD signalling and histone deacetylation. These data highlight functionally rational and novel combinatorial possibilities for children with ACVR1-mutant DMG, with systematic preclinical assessment required for prioritisation for the clinic.

AMH inhibits androgen production in human theca cells

Both excessive ovarian production of AMH and androgen are important features of polycystic ovary syndrome (PCOS). Present study aimed to explore the direct effect of AMH on androgen production in human theca cells. Primary cultured human theca cells were treated with AMH, an ALK2 (the BMP type 1 receptor) inhibitor and an ALK5 (the TGFβ type 1 receptor) inhibitor. AMH significantly suppresses the expression of the androgen synthesis-related enzyme CYP17A1 and reduces the production of androstenedione and testosterone in normal human theca cells and PCOS theca cells. Inhibitors of ALK2/3 and ALK5 antagonize the effect of AMH on the expression of CYP17A1. Although both ALK5 and ALK2 interact with AMHR2 in the presence of AMH, AMH activated neither TGFβR-Smads (Smad 2/3) nor BMPR-Smads (Smad 1/5/8). Our data suggested that AMH suppresses androgen synthesis-related enzyme CYP17A1 expression and inhibits androgen production in human theca cells, which process may be mediated by ALK2 and ALK5.

Suppressive Role of ACVR1/ALK2 in Basal and TGFβ1-Induced Cell Migration in Pancreatic Ductal Adenocarcinoma Cells and Identification of a Self-Perpetuating Autoregulatory Loop Involving the Small GTPase RAC1b.

Pancreatic ductal adenocarcinoma (PDAC) cells are known for their high invasive/metastatic potential, which is regulated in part by the transforming growth factor β1 (TGFβ1). The involvement of at least two type I receptors, ALK5 and ALK2, that transmit downstream signals of the TGFβ via different Smad proteins, SMAD2/3 and SMAD1/5, respectively, poses the issue of their relative contribution in regulating cell motility. Real-time cell migration assays revealed that the selective inhibition of ALK2 by RNAi or dominant-negative interference with a kinase-dead mutant (ALK2-K233R) strongly enhanced the cells’ migratory activity in the absence or presence of TGFβ1 stimulation. Ectopic ALK2-K233R expression was associated with an increase in the protein levels of RAC1 and its alternatively spliced isoform, RAC1b, both of which are implicated in driving cell migration and invasion. Conversely, the RNAi-mediated knockdown or CRISPR/Cas9-mediated knockout of RAC1b resulted in the upregulation of the expression of ALK2, but not that of the related BMP type I receptors, ALK3 or ALK6, and elevated the phosphorylation of SMAD1/5. PDAC is a heterogeneous disease encompassing tumors with different histomorphological subtypes, ranging from epithelial/classical to extremely mesenchymal. Upon treatment of various established and primary PDAC cell lines representing these subtypes with the ALK2 inhibitor, LDN-193189, well-differentiated, epithelial cell lines responded with a much stronger increase in the basal and TGFβ1-dependent migratory activity than poorly differentiated, mesenchymal ones. These data show that (i) ALK2 inhibits migration by suppressing RAC1/RAC1b proteins, (ii) ALK2 and RAC1b act together in a self-perpetuating the autoregulatory negative feedback loop to mutually control their expression, and (iii) the ALK2 antimigratory function appears to be particularly crucial in protecting epithelial subtype cells from becoming invasive, both spontaneously and in a TGFβ-rich tumor microenvironment.

AML-326 Novel FLT3-ALK2 Dual Inhibitor TP-0184 Inhibits Leukemia Growth by Targeting Serine Biosynthesis in FLT3-ITD-Positive AML Cells

FMS-like tyrosine kinase 3 (FLT3) internal tandem duplication (ITD) inhibitors have been studied; however, molecular factors contributing to this resistance are unknown. i) To investigate the clinical significance of BMP type 1 receptor ALK2 in AML patients with FLT3-ITD mutations. ii) To elucidate the therapeutic effect of FLT3-ALK2 dual inhibitor TP-0184 on leukemia growth. To determine whether ALK2 is a potential target in FLT3-mutated AML patients, we analyzed OHSU and TCGA datasets. We treated AML cell lines with FLT3-WT or -ITD mutations with ALK2 inhibitors and measured their effect on cell cycle and proliferation. To determine the mechanism of TP-0184, we measured the activation of FLT3 downstream signaling by using western blotting and RNA sequencing. Further, we performed kinase profiling to understand the binding specificity of TP-0184 with 11 different FLT3 mutants. Finally, we investigated the effect of TP-0184 on AML growth in vivo using FLT3-mutated PDX and xenograft models. Analysis of AML datasets showed that ALK2 is significantly upregulated in AML patients with FLT3 mutations compared to those with WT-FLT3 (P<0.00001) and predicts poor overall survival (P=0.05). Treatment of FLT3-WT and -mutated AML cell lines with the ALK2 inhibitors LDN-212854 and TP-0184 resulted in significant inhibition of FLT3-ITD-mutant cell growth at low concentrations (IC50<25 nM), while WT-FLT3 cells were affected only at high concentrations (IC50>100 nM). Interestingly, TP-0184 induced G1/G0 arrest in AML cell lines with FLT-ITD mutations but had minimal to no effect in FLT3-WT AML cells. Further, we observed that treatment with TP-0184 in AML cell lines significantly inhibited multiple signaling proteins downstream of FLT3, such as p-STAT5 and p-ERK, as well as p-PI3K, p-mTOR, and p-S6K. Gene expression analysis revealed that treatment with TP-0184 in FLT3-ITD cell lines significantly downregulated the serine biosynthesis pathway. Lastly, treatment with TP-0184 significantly prolonged the survival of FLT3-ITD-mutated AML-bearing mice (P<0.0001). Our data indicate that ALK2 is a prognostic marker in FLT3-mutated AML. TP-0184 inhibits cell proliferation by inhibiting FLT3 downstream signaling pathways in AML cells. Kinase assays confirmed that TP-0184 is a highly specific FLT3-ALK2 dual inhibitor. TP-0184 inhibits AML growth in FLT3-mutated PDX and xenograft models.

DIPG-40. Combined pharmacological and genetic screening to identify dependencies and combinations in ACVR1-mutant diffuse midline glioma

Somatic mutations in ACVR1, which encodes the serine/threonine kinase ALK2, are found in 20-25% of DMG-H3K27 patients. Treatment of ACVR1-mutant patient-derived models with multiple chemotypes of ALK2 inhibitors (ALK2i) results in reduced cell viability in vitro and extended survival in orthotopic xenografts in vivo but, as single agents, these inhibitors were unable to achieve a complete anti-tumour response. Recently we reported that combinatorial treatment of ACVR1-mutant DIPG cells with vandetanib (RTK inhibitor) and everolimus (mTOR/ABC transporter inhibitor) was synergistic both in vitro and in vivo and was shown to be a feasible combination to trial clinically in this setting. To identify specific dependencies in ACVR1-mutant cells which may be translatable with novel synergistic drug combinations alongside ALK2i, we have implemented both candidate and unbiased drug and genetic screening approaches. Using a panel of patient-derived ACVR1-mutant and wild-type models, we identified synergy between multiple chemotypes of ALK2i (M4K2009/LDN-214117) and PI3K/mTOR (AZD8055/everolimus) and MEK inhibitors (trametinib), reflecting the common co-segregation of PIK3CA/PIK3R1 alterations in these tumours. Whole-genome CRISPR/Cas9 screening of ACVR1-mutant SU-DIPG-IV cells in combination with two ALK2i (M4K2009/LDN-193189), confirmed a specific MTOR genetic dependency, as well as for the protein phosphatase regulatory subunit PPP2R1A, known to play a role in MAPK pathway activation. Additional hits include the serine/threonine kinase PKMYT1, a negative regulator of the G2/M checkpoint via a functionally redundant phosphorylation of CDK1/CCNB1 alongside WEE1; confirmatory drug assays with the WEE1 inhibitor AZD1775 resulted in a synergistic interaction with ALK2i in ACVR1-mutant cells. Hits were integrated with DepMap using ‘gene-effect’ scores (Chronos) enabling filtering of common essential genes. Preliminary pathway enrichment analysis (MAGeCKFlute) identified ALK2i-specific vulnerabilities involving TGFB1/SMAD signalling and histone deacetylation. These data highlight functionally rational and novel combinatorial possibilities for children with ACVR1-mutant DMG, with systematic preclinical assessment required for prioritisation for the clinic.

Dual Nickel/Photoredox-Catalyzed Deaminative Cross-Coupling of Sterically Hindered Primary Amines.

We report a method to activate α-3° amines for deaminative arylation via condensation with an electron-rich aldehyde and merge this reactivity with nickel metallaphotoredox to generate benzylic quaternary centers, a common motif in pharmaceuticals and natural products. The reaction is accelerated by added ammonium salts. Evidence is provided in support of two roles for the additive: inhibition of nickel black formation and acceleration of the overall reaction rate. We demonstrate a robust scope of amine and haloarene coupling partners and show an expedited synthesis of ALK2 inhibitors.

TP-0184, a Novel FLT3-ALK2 Dual Inhibitor, Targets Amino Acid Transport and Biosynthesis in AML Cells and Sensitizes AML Cells to Chemotherapy and BCL2 Inhibition

Background FMS-like tyrosine kinase 3 (FLT3), a transmembrane receptor tyrosine kinase that is frequently mutated in AML, is associated with poor prognosis. Inhibitors of FLT3 internal tandem duplication (ITD) mutants and wild-type (WT) FLT3 have been studied, but their clinical usefulness is limited owing to treatment resistance. However, the molecular factors contributing to this resistance are unknown. We reported that AML cells induce osteogenic differentiation of bone marrow-derived mesenchymal stromal cells through the bone morphogenetic protein (BMP)-mediated signaling pathway, promoting leukemic growth. However, the effects of targeting BMP signaling in patients with FLT3-mutated AML are unexplored. Here, we hypothesized that the BMP type 1 receptor ALK2 is a key biomarker and a therapeutic target in AML patients with FLT3-ITD mutations and that the FLT3-ALK2 dual inhibitor TP-0184 inhibits leukemia growth.Methods: To determine whether ALK2 is a potential target in AML patients with FLT3-ITD mutations, we analyzed gene expression datasets (OHSU and TCGA). We treated 9 AML cell lines with FLT3-WT or ITD mutations with varying doses of ALK2 inhibitors (LDN-212854 or TP-0184) and measured their effect on cell proliferation and the cell cycle. To determine the mechanism of TP-0184-mediated cell cycle arrest, we measured activation of FLT3 downstream signaling by using Western blotting and RNA sequencing. IncuCyte live-cell imaging was used to determine the apoptotic effects of TP-0184 in combination with chemotherapy or targeted therapy agents. Further, we performed human RTK kinase binding assay to understand the binding specificity of TP-0184 with 11 different FLT3 mutants. Finally, the effect of TP-0184 on AML growth in vivo was investigated using an FLT3-ITD positive AML xenograft model (MOLM13).Results: Analysis of AML datasets showed that ALK2 is significantly upregulated in AML patients with FLT3 mutations compared to those with WT-FLT3 (p < 0.00001) and predicts poor overall survival (p = 0.05). Validating these findings, we found higher ALK2 mRNA expression in AML cell lines with FLT3-ITD mutations than in those with WT-FLT3 (p = 0.039). This suggests that ALK2 could serve as a therapeutic target in AML with FLT3-ITD mutation. Treatment of FLT3-WT and -mutated AML cell lines with the ALK2 inhibitors LDN-212854 and TP-0184 resulted in significant inhibition of FLT3-ITD-mutant cell growth at low concentrations (IC50<25nM), while WT-FLT3 cells were affected only at high concentrations (IC50>100nM). Interestingly, TP-0184 was 10-fold more potent in inhibiting AML cell proliferation than was LDN-212854. TP-0184 induced G1/G0 arrest in AML cell lines with FLT-ITD mutations but had minimal to no effect in FLT3-WT AML cells, suggesting that AML cell lines with FLT3-ITD mutations depend on ALK2 for their survival. Further, we observed that treatment with TP-0184 in AML cell lines significantly inhibited multiple signaling proteins downstream of FLT3, such as p-STAT5, p-MKK3, and p-ERK, as well as p-PI3K, p-AKT, p-mTOR, p-4E-BP1, and p-S6K. Gene expression analysis revealed that treatment with TP-0184 in FLT3-ITD cell lines significantly downregulated the serine biosynthesis pathway, which is essential in these cells (Bjelosevic S. et al., Cancer Discov, 2021). Moreover, molecular docking and kinase-binding studies revealed that TP-0184 is bound to wild-type FLT3 as well as most of the FLT3 mutants with dissociation constants (KD) less than 5nM. These data suggest that TP-0184 inhibits both mutant FLT3 and ALK2 in AML cells. Interestingly, TP-0184 plus chemotherapy showed a synergistic effect only in FLT3-ITD cell lines, whereas TP-0184 plus the BCL2 inhibitor, venetoclax was synergistic in both FLT3-ITD and FLT3-WT cell lines. Lastly, treatment with TP-0184 inhibited AML growth and significantly prolonged survival of FLT3-ITD-mutated AML-bearing mice in a dose-dependent manner (p <0.0001).Conclusion: Our data indicate that ALK2 is a prognostic marker for AML patients with FLT3-ITD mutations. TP-0184 significantly inhibits cell proliferation by inhibiting signaling pathways downstream of FLT3, including serine biosynthesis, in AML cells. Kinase assays confirmed that TP-0184 is a highly specific FLT3 inhibitor as well as an ALK2 inhibitor. TP-0184 sensitizes AML cells to chemotherapeutic agents and targeted therapy and inhibits AML growth in vivo. DisclosuresFoulks: Sumitomo Dainippon Pharma Oncology: Patents & Royalties: WO2021102343A1; Sumitomo Dainippon Pharma Oncology: Patents & Royalties: CA3103995A1; Sumitomo Dainippon Pharma Oncology: Patents & Royalties: US11040038B2. Warner: Sumitomo Dainippon Pharma Oncology: Patents & Royalties: US11040038B2; Sumitomo Dainippon Pharma Oncology: Patents & Royalties: US10752594B2; Sumitomo Dainippon Pharma Oncology: Patents & Royalties: CA3103995A1; Sumitomo Dainippon Pharma Oncology: Patents & Royalties: WO2021102343A1. Battula: Tolero Pharmaceuticals: Research Funding.

Discovery of novel ALK2 inhibitors of pyrazolo-pyrimidines: A computational study

ALK2 is a serine/threonine kinase, involved in different signaling pathways and associated with cell proliferation and differentiation. The present study includes development of pharmacophore, 3-D QSAR, docking and virtual screening studies on 30 different pyrazolo[1,5-a]pyrimidine derivatives. The pharmacophore study provides ARRR_2 hypothesis with four different features essential for ALK2 kinase inhibitory activity. The 3 D-QSAR study determined the statistically significant model by using partial least-square regression (PLS) method with R 2 value of 0.9711 and Q 2 value of 0.6846. Validation of 3 D-QSAR has been performed by LOO cross-validation method where with R2CV value of 0.56. The virtual screening study on ZINC database provides compounds such as ZINC66091638, ZINC43524105, ZINC19458227 and ZINC72441013 involved good binding interactions (docking scores −8.91, −7.40, −8.43, and −9.47, respectively) with ALK2 kinase (PDB ID: 3Q4U). The docking study of pyrazolo-pyrimidines derivatives found potent compounds, 7i, 13r, 13d, and 21 with docking scores −9.83, −9.75, −9.76, and −9.75, respectively. The important interactions with amino acid residues were HID 286, ASN341. ADME properties further assist to provide important structural features of ALK2 kinase. The present study may be help to medicinal scientists in the direction to develop potent inhibitors against ALK2 kinase. Communicated by Ramaswamy H. Sarma

Abstract CT216: A Phase 1/2 Study of INCB000928 as Monotherapy or in Combination with Ruxolitinib in Patients with Anemia Due to Myelofibrosis (INCB 00928-104)

Abstract Background: Anemia represents a therapeutic challenge in patients with myelofibrosis (MF). ALK2 activation is associated with elevated hepcidin, which may contribute to anemia of chronic disease and anemia due to hematologic malignancies, and is associated with increased transfusion rate and reduced overall survival. This phase 1/2, open-label, multicenter, dose-escalation/dose-expansion study will evaluate the safety and tolerability of INCB000928, a potent, highly selective, ALK2 inhibitor, as monotherapy or combined with ruxolitinib in patients with anemia due to MF (INCB 00928-104; NCT04455841). Methods: Patients with histologically confirmed primary/secondary MF presenting with transfusion-dependent or symptomatic anemia will receive oral INCB000928 either alone (treatment group [TG] A) or combined with ruxolitinib (TGB). In TGA, patients must have intermediate (INT)-2 or high-risk (per Dynamic International Prognostic Scoring System [DIPSS]) disease that is intolerant, resistant, refractory, or has lost response to prior JAK inhibitor therapy (≥12 weeks). In TGB, patients must have received stable ruxolitinib therapy for ≥12 consecutive weeks before first dose and have INT-1/INT-2, or high-risk disease. Eligibility also requires age ≥18 y, ECOG PS 0-1 (dose-escalation) or 0-2 (dose-expansion), life expectancy &amp;gt;6 months, no other hematologic malignancy, no prior stem cell transplantation, no major surgery within 28 days, and no prior disease-directed therapy within 5 half-lives or 28 days of first dose. In Part 1 (dose escalation), TGA will receive INCB000928 monotherapy starting at 50 mg/day (28-day cycles). Dose-escalation will follow a Bayesian optimal-interval design to determine the maximum tolerated dose (MTD) and/or recommended dose for expansion (RDE). Dose increases not exceeding 2-fold will continue until Grade ≥2 treatment-related toxicity occurs. TGB will receive INCB000928 plus ruxolitinib; INCB000928 dose escalation will start 2 dose levels below the highest dose determined to be safe and tolerable in TGA. In Part 2 (dose expansion), the RDE in TGB will be evaluated in combination with ruxolitinib in ~25 patients; treatment will continue for ≤12 months, and may continue if clinically beneficial and no progression occurs. Primary objective is to determine the safety and tolerability of INCB000928 as monotherapy or combined with ruxolitinib. Secondary objectives are to determine the efficacy of INCB000928 as monotherapy or combined with ruxolitinib (anemia response, duration of anemia response, mean change from baseline in hemoglobin, and RBC transfusion rate through weeks 24 and 48); evaluate INCB000928 pharmacokinetics; and evaluate effects of INCB000928 as monotherapy or combined with ruxolitinib on hepcidin levels and other measures of iron homeostasis and erythropoiesis. Citation Format: Stephen T. Oh, Jean-Jacques Kiladjian, Francesca Palandri, Jason R. Gotlib, Sanjay Mohan, Haris Ali, Ekatherine Asatiani, Francis Seguy, Feng Zhou, Srdan Verstovsek. A Phase 1/2 Study of INCB000928 as Monotherapy or in Combination with Ruxolitinib in Patients with Anemia Due to Myelofibrosis (INCB 00928-104) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT216.

MODL-20. A BIOBANK OF ~100 PATIENT-DERIVED MODELS REPRESENTING BIOLOGICAL HETEROGENEITY AND DISTINCT THERAPEUTIC DEPENDENCIES IN PAEDIATRIC HIGH GRADE GLIOMA AND DIPG

Paediatric high-grade glioma comprise multiple biological and clinical subgroups, the majority of which urgently require novel therapies. Patient-derived models represent useful tools for mechanistic and preclinical investigations based upon their retention of key genetic/epigenetic features and their amenability to high-throughput approaches. We have collected ~100 in vitro models representing multiple subtypes (H3.3/H3.2/H3.1K27M, H3.3G34R/V, BRAF, MYCN_amp, NTRK_fusion, hypermutator, others) established under 2D (laminin) and/or 3D (neurosphere) conditions, credentialed by phenotypic (growth, invasion/migration) and molecular (methylation array, DNA sequencing, RNAseq) comparison to the original tumour sample. These were derived from patients at our local hospitals (n=29), as part of national co-clinical trials (n=19), from international collaborating centres (n=11), or shared directly by research groups worldwide (n=45). These have variously been subjected to pharmacological (approved/experimental drug libraries) and/or genetic screening (whole-genome CRISPR) to identify specific biological dependencies. Many have been established as orthotopic xenografts in vivo (PDX), with detailed pathological and radiological correlations with the clinical disease, and with tumorigenic latencies ranging from 48–435 days. This resource has allowed us to identify genotype-specific synthetic lethalities and responses to targeted inhibitors, including olaparib (PARP) with ATRX, nutlin-3 (MDM2) with PPM1D, AZD1775 (WEE1) with TP53, and CYC065 (CDK9) with MYCN-amplification. Combinatorial screening highlighted synergies in ACVR1-mutant DIPG between novel ALK2 inhibitors and ONC201 (DRD2). Rapid screening allows for feedback of drug sensitivities to treating clinicians at relapse, whilst mechanistic underpinning of these interactions and use of the models to identify specific mediators of resistance will allow for rational future trial design.

Characterization of INCB00928, a Potent and Selective ALK2 Inhibitor for the Treatment of Anemia

A significant population of patients with myelofibrosis (MF) develop anemia and either require red blood cell (RBC) transfusions or have an inadequate response to the currently available therapies and become transfusion-dependent. In patients with MF, elevated levels of serum hepcidin, a key iron regulatory hormone, is associated with increased dependence on RBC transfusions and reduced overall survival. Elevated hepcidin expression has also been observed to cause severe functional iron deficiency anemia and is central to the pathophysiology of anemia of chronic disease. Thus, to ensure proper maintenance of iron homeostasis, hepcidin levels are tightly regulated. Specifically, the production of hepcidin is controlled by the bone morphogenetic protein (BMP) type I receptor ACVR1, a gene that encodes the serine/threonine kinase ALK2. In preclinical models, knockdown or complete loss of ALK2 decreases hepcidin production resulting in elevated serum iron levels. In this study, we report characterization of INCB00928, a novel small molecule inhibitor of ALK2 for the treatment of anemia. INCB00928 was observed to have subnanomolar activity against ALK2 and selectivity over ALK1 and ALK3 in biochemical enzyme assays. In cell-based profiling studies, INCB00928 inhibited ALK2 potently and selectively over ALK1 and ALK3 as determined by the inhibition of ligand-induced SMAD pathway signaling. Importantly, in both an immortalized human liver cell line as well as primary human hepatocytes, INCB00928 inhibited BMP-induced production of hepcidin with nanomolar activity. INCB00928 was also observed to have suitable absorption, distribution, metabolism, and excretion properties to be dosed in in vivo rodent studies. In tumor- and inflammation-induced mouse models of anemia, INCB00928 improved RBC count, hemoglobin, and hematocrit levels while decreasing hepcidin levels in a dose-dependent manner. Additionally, consistent with the improved symptoms of anemia, pSMAD1/5 inhibition was observed in a dose-dependent manner in liver tissues collected from INCB00928-treated mice. In summary, INCB00928 is a potent, selective, and orally available small molecule inhibitor of ALK2, which significantly reduces the production of hepcidin in human liver cells, primary hepatocytes, and in rodent models of anemia. For the majority of patients with MF, the management of anemia remains an unmet need. The preclinical findings from this study suggest ALK2 kinase inhibition with INCB00928 may be a promising novel treatment to reduce the production of hepcidin and improve MF-related anemia in humans, thus warranting further investigation. Disclosures Chen: Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Stubbs:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Pusey:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Wen:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Collins:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Kapilashrami:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Rupar:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Thekkat:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Lin:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Bowman:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Yang:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Diamond:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Yeleswaram:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Kim:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Koblish:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Chen:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company. Wee:Incyte Corporation: Current Employment, Current equity holder in publicly-traded company.

Targeting ALK2: An Open Science Approach to Developing Therapeutics for the Treatment of Diffuse Intrinsic Pontine Glioma.

Diffuse intrinsic pontine glioma is an aggressive pediatric cancer for which no effective chemotherapeutic drugs exist. Analysis of the genomic landscape of this disease has led to the identification of the serine/threonine kinase ALK2 as a potential target for therapeutic intervention. In this work, we adopted an open science approach to develop a series of potent type I inhibitors of ALK2 which are orally bio-available and brain-penetrant. Initial efforts resulted in the discovery of M4K2009, an analogue of the previously reported ALK2 inhibitor LDN-214117. Although highly selective for ALK2 over the TGF-βR1 receptor ALK5, M4K2009 is also moderately active against the hERG potassium channel. Varying the substituents of the trimethoxyphenyl moiety gave rise to an equipotent benzamide analogue M4K2149 with reduced off-target affinity for the ion channel. Additional modifications yielded 2-fluoro-6-methoxybenzamide derivatives (26a–c), which possess high inhibitory activity against ALK2, excellent selectivity, and superior pharmacokinetic profiles.

MGMT Expression Contributes to Temozolomide Resistance in H3K27M-Mutant Diffuse Midline Gliomas.

Diffuse midline gliomas (DMGs) show resistance to many chemotherapeutic agents including temozolomide (TMZ). Histone gene mutations in DMGs trigger epigenetic changes including DNA hypomethylation, one of which is a frequent lack of O6-methyl-guanine-DNA methyltransferase (MGMT) promoter methylation, resulting in increased MGMT expression. We established the NGT16 cell line with HIST1H3B K27M and ACVR1 G328E gene mutations from a DMG patient and used this cell line and other DMG cell lines with H3F3A gene mutation (SF7761, SF8628, JHH-DIPG1) to analyze MGMT promoter methylation, MGMT protein expression, and response to TMZ. Three out of 4 DMG cell lines (NGT16, SF8628, and JHH-DIPG1) had unmethylated MGMT promoter, increased MGMT expression, and showed resistance to TMZ treatment. SF7761 cells with H3F3A gene mutation showed MGMT promoter methylation, lacked MGMT expression, and sensitivity to TMZ treatment. NGT16 line showed response to ALK2 inhibitor K02288 treatment in vitro. We confirmed in vitro that MGMT expression contributes to TMZ resistance in DMG cell lines. There is an urgent need to develop new strategies to treat TMZ-resistant DMGs.