Combining VPS34 inhibitors with STING agonists enhances type I interferon signaling and anti-tumor efficacy

An immunosuppressive tumor microenvironment promotes tumor growth and is one of the main factors limiting the response to cancer immunotherapy. We have previously reported that inhibition of vacuolar protein sorting 34 (VPS34), a crucial lipid kinase in the autophagy/endosomal trafficking pathway, decreases tumor growth in several cancer models, increases infiltration of immune cells and sensitizes tumors to anti-programmed cell death protein 1/programmed cell death 1 ligand 1 therapy by upregulation of C-C motif chemokine 5 (CCL5) and C-X-C motif chemokine 10 (CXCL10) chemokines. The purpose of this study was to investigate the signaling mechanism leading to the VPS34-dependent chemokine increase. NanoString gene expression analysis was applied to tumors from mice treated with the VPS34 inhibitor SB02024 to identify key pathways involved in the anti-tumor response. We showed that VPS34 inhibitors increased the secretion of T-cell-recruitment chemokines in a cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes protein (STING)-dependent manner in cancer cells. Both pharmacological and small interfering RNA (siRNA)-mediated VPS34 inhibition increased cGAS/STING-mediated expression and secretion of CCL5 and CXCL10. The combination of VPS34 inhibitor and STING agonist further induced cytokine release in both human and murine cancer cells as well as monocytic or dendritic innate immune cells. Finally, the VPS34 inhibitor SB02024 sensitized B16-F10 tumor-bearing mice to STING agonist treatment and significantly improved mice survival. These results show that VPS34 inhibition augments the cGAS/STING pathway, leading to greater tumor control through immune-mediated mechanisms. We propose that pharmacological VPS34 inhibition may synergize with emerging therapies targeting the cGAS/STING pathway.

Inhibition of ULK1/2 and KRAS G12C controls tumor growth in preclinical models of lung cancer

Mutational activation of KRAS occurs commonly in lung carcinogenesis and, with the recent FDA approval of covalent inhibitors of KRAS G12C such as sotorasib or adagrasib, KRAS oncoproteins are important pharmacological targets in non-small cell lung cancer (NSCLC). However, not all KRAS G12C -driven NSCLCs respond to these inhibitors, and the emergence of drug resistance in those patients that do respond can be rapid and pleiotropic. Hence, based on a backbone of covalent inhibition of KRAS G12C , efforts are underway to develop effective combination therapies. Here we report that inhibition of KRAS G12C signaling increases autophagy in KRAS G12C expressing lung cancer cells. Moreover, the combination of DCC-3116, a selective ULK1/2 inhibitor, plus sotorasib displays cooperative/synergistic suppression of human KRAS G12C -driven lung cancer cell proliferation in vitro and superior tumor control in vivo . Additionally, in genetically engineered mouse models of KRAS G12C -driven NSCLC, inhibition of either KRAS G12C or ULK1/2 decreases tumor burden and increases mouse survival. Consequently, these data suggest that ULK1/2-mediated autophagy is a pharmacologically actionable cytoprotective stress response to inhibition of KRAS G12C in lung cancer.

Abstract 1639: DP-9149, an investigational small molecule modulator of the Integrated Stress Response kinase GCN2, pre-clinically causes solid tumor growth inhibition as a single agent and regression in combination with standard of care agents

Background: The Integrated Stress Response (ISR) is one of the major adaptive stress response pathways in cancer and plays an important role in cell fate determination. Oncogene addicted solid tumors are under high stress levels, both extrinsic as well as intrinsic, and are dependent on a well-balanced ISR pathway activity to cope with the high demand for accelerated growth. The ISR is well known to be a double edge sword of survival and cell death and depending on context, the activation of the ISR kinase, GCN2, and downstream pathway can have either cytoprotective or cytotoxic effects. Given the context-dependent nature of the ISR pathway, the inhibition or stimulation of GCN2 in solid tumors can be pharmacologically leveraged to induce anti-tumoral effects.

Methods: Modulation of ISR kinases was characterized using enzymatic assays. Kinome selectivity profiling was determined using enzymatic and cellular assays. Cellular modulation of the ISR pathway (phospho-GCN2, ATF4, CHOP) or the apoptosis pathway (PARP and Caspase3/7) was assessed via Western blot or ELISA. In vivo upregulation of tumoral ATF4 was determined in a fibrosarcoma PK/PD xenograft model. In vivo inhibition of tumor growth was determined in solid tumor xenografts.

Results: Selective and potent modulators of GCN2 kinase with favorable drug-like properties were designed. These compounds were found to upregulate components of the ISR pathway (phospho-GCN2, ATF4, CHOP). The mechanism by which GCN2 modulator DP-9149 treatment induced the ISR pathway was found to be through the direct binding and activation of GCN2. Upregulation of the ISR pathway downstream of GCN2 led to induction of a programmed cell death pathway in oncogene-driven solid tumor cell lines in vitro. DP-9149-mediated activation of the ISR pathway led to cell growth arrest both as a single agent and in combination with standard-of-care (SOC) agents. Furthermore, oral dosing of DP-9149 in RAS mutant and other oncogene-driven xenograft models in vivo induced ATF4, and significantly inhibited tumor growth as a single agent and in combination with SOC agents. Additionally, therapeutic agents targeting the tumor microenvironment, including anti-angiogenic agents, synergized with DP-9149 to induce tumor regressions in vivo.

Conclusions: The ISR is a targetable vulnerability in oncogene addicted solid tumors. Upregulating the ISR by paradoxical activation of the ISR family member kinase, GCN2, by DP-9149 can be leveraged as a novel mechanism to cause anti-tumoral effects in solid tumors in vitro and in vivo, likely through the induction of an unresolved stress response. In particular, DP-9149 exhibited robust activity in RAS mutant cancers and in VHL-mutant renal cancers as a single agent and in combination with SOC agents in vivo.

Citation Format: Gada Al-Ani, Qi Groer, Kristin M. Elliott, Aaron J. Rudeen, Patrick C. Kearney, Jeffery D. Zwicker, Yu Mi Ahn, Stacie L. Bulfer, Cale L. Heiniger, Molly M. Hood, Salim Javid, Joshua W. Large, Max D. Petty, Kristen L. Stoltz, Bertrand Le Bourdonnec, Bryan D. Smith, Daniel L. Flynn. DP-9149, an investigational small molecule modulator of the Integrated Stress Response kinase GCN2, pre-clinically causes solid tumor growth inhibition as a single agent and regression in combination with standard of care agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1639.

Abstract 4033: Pan-exon mutant KIT inhibitor DCC-3009 demonstrates tumor regressions in preclinical gastrointestinal stromal tumor models

Introduction: Gastrointestinal stromal tumors (GISTs) are typically driven by primary mutations in KIT exons 9 or 11. Heterogeneous drug-resistant secondary mutations arise in patients treated with FDA approved KIT inhibitors, including imatinib and sunitinib. Drug resistant secondary mutations are found at multiple regions in the ATP pocket (encoded by exons 13 and 14) or activation switch (encoded by exons 17 and 18) of KIT kinase. In addition, multiple drug-resistant clones can arise within a tumor or in metastatic tumor sites. An inhibitor that can broadly and potently inhibit the spectrum of KIT mutations is highly sought. Ripretinib has been FDA approved as a 4th line treatment for GIST and has broad activity against KIT mutations, including clinical potency in patients with mutations in KIT exons 11, 17, or 18. DCC-3009 was designed as a next generation KIT inhibitor that broadly and potently inhibits primary KIT mutations in exons 9 and 11 and secondary drug-resistant mutations across exons 13, 14, 17, and 18. DCC-3009 is a potent and selective inhibitor in enzyme and cell-based assays, and has demonstrated efficacy in xenograft models driven by drug resistant KIT mutations.

Methods: DCC-3009 was tested for inhibition of KIT mutants using standard enzyme and cell-based assays. Levels of phosphorylated KIT were determined by Western blot or ELISA. Proliferation was measured using the fluorescent dye resazurin. KIT mutant xenograft or patient-derived xenograft models were performed at Crown Biosciences or Labcorp, AAALAC accredited facilities, with the approval of Animal Care and Use Committees.

Results: In BaF3 cells transfected with KIT mutants, DCC-3009 was shown to potently inhibit the spectrum of known primary and secondary drug-resistant mutations in GIST. The pan-mutant KIT profile of DCC-3009 was shown in vitro to be superior to 2nd and 3rd line standard of care therapies sunitinib and regorafenib. DCC-3009 was selective for KIT when screened against a large panel of kinases. DCC-3009 has optimized pharmaceutical properties for oral administration. In pharmacokinetic/pharmacodynamic studies DCC-3009 achieved sufficient free drug levels to significantly inhibit drug-resistant KIT mutants for 12 hr post dose. In xenograft studies, treatment with DCC-3009 twice daily led to tumor regression in drug-resistant models with KIT exon 9/13, 11/13 or 11/17 mutations.

Conclusions: DCC-3009 is a pan-exon mutant KIT inhibitor exhibiting high potency in KIT mutants in pre-clinical models spanning exons 9, 11, 13, 14, 17 and 18. In vivo, DCC-3009 exhibited efficacy in drug-resistant models with KIT exon 9/13, 11/13 or 11/17 mutations. Based on this profile, DCC-3009 has entered formal preclinical development.

Citation Format: Bryan D. Smith, Subha Vogeti, Timothy M. Caldwell, Hanumaiah Telikepalli, Yu Mi Ahn, Gada Al-Ani, Stacie L. Bulfer, Andrew Greenwood, Cale L. Heiniger, Joshua W. Large, Cynthia B. Leary, Wei-Ping Lu, Kylie Luther, William C. Patt, Max D. Petty, Yeni K. Romero, Forrest A. Stanley, Kristen L. Stoltz, Daniel C. Tanner, Sihyung Yang, Yu Zhan, Bertrand Le Bourdonnec, Daniel L. Flynn. Pan-exon mutant KIT inhibitor DCC-3009 demonstrates tumor regressions in preclinical gastrointestinal stromal tumor models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4033.

Abstract 4045: DCC-3084, a RAF dimer inhibitor, broadly inhibits BRAF class I, II, III, BRAF fusions, and RAS-driven solid tumors leading to tumor regression in preclinical models

Background: Mutations in the RAS/MAPK pathway are a frequent driver of cancer, with oncogenic RAS or RAF mutations occurring in >30% of all cancers. First generation BRAF inhibitors are approved for use for tumors with Class I BRAF mutations (V600X). However, these drugs are not efficacious in RAF dimer mutant and RAS mutant cancers due to paradoxical activation of RAF dimers. Herein, we describe DCC-3084, a potent and selective investigational Switch Control inhibitor of BRAF and CRAF kinase dimers that targets Class I, II and III BRAF mutations, BRAF fusions, and BRAF/CRAF heterodimers. DCC-3084 combines with inhibitors of additional nodes in the MAPK pathway to potentially target a large unmet medical need in RAS and RAF mutant cancers.

Methods: Inhibition of RAF kinases, including off-rate analysis, was measured using recombinant enzymes. X-ray crystallography was used for structure-based drug design. Cellular proliferation was measured using resazurin to monitor cell viability. Synergy in cells was measured using BLISS scores and curve shift analysis. Inhibition of ERK or RSK phosphorylation was measured by AlphaLISA or ELISA. Pharmacokinetics (PK) in the plasma, brain and CSF compartments were measured following oral dosing in Wistar rats. RAF and RAS mutant mouse xenograft models were used to assess PK, pharmacodynamics (PD), and efficacy.

Results: DCC-3084 is a potent and selective Switch Control inhibitor of RAF dimers that was designed to target Class I, II, III BRAF mutants, BRAF fusions, and BRAF/CRAF heterodimers. DCC-3084 inhibits BRAF and CRAF, exhibiting slow off-rates (t1/2 >20 hr). Potent single-agent inhibition of MAPK pathway signaling and cellular proliferation was observed in a wide range of Class I, II, III BRAF and BRAF fusion altered cell lines. Synergy was observed in combination with inhibitors of other nodes in the RAS/MAPK pathway in RAS mutant cell lines. DCC-3084 was demonstrated to be CNS penetrable and exhibited dose dependent oral exposure with robust inhibition of the RAS/MAPK pathway in PK/PD models. DCC-3084 accumulated in tumor tissue relative to plasma, further demonstrating a favorable pharmaceutical profile. Oral treatment of DCC-3084 as a single agent resulted in tumor regression in BRAF mutant and KRAS Q61K mutant mouse xenograft models and tumor growth inhibition in KRAS G12C/D mutant models. Additionally, DCC-3084 in combination with a MEKi resulted in tumor regression in KRAS mutant models.

Conclusions: The Switch Control inhibitor DCC-3084 broadly inhibits Class I, II and III BRAF mutations, BRAF fusions, and BRAF/CRAF heterodimers leading to tumor regression in preclinical models. The overall preclinical profile of DCC-3084 supports IND-enabling activities towards clinical development in a key area of unmet medical need in RAS and RAF mutant cancers.

Citation Format: Stacie L. Bulfer, Bertrand Le Bourdonnec, Jeffery D. Zwicker, Yu Mi Ahn, Gada Al-Ani, Hikmat Al-Hashimi, Chase Crawley, Kristin M. Elliott, Saqib Faisal, Andrew M. Harned, Cale L. Heiniger, Molly M. Hood, Salim Javed, Michael Kennedy, Joshua W. Large, Cynthia B. Leary, Wei-Ping Lu, Kylie Luther, Max D. Petty, Hunter R. Picard, Justin T. Proto, Yeni K. Romero, Forrest A. Stanley, Kristen L. Stoltz, Daniel C. Tanner, Hanumaiah Telikepalli, Mary J. Timson, Lakshminarayana Vogeti, Subha Vogeti, Sihyung Yang, Lexy H. Zhong, Bryan D. Smith, Daniel L. Flynn. DCC-3084, a RAF dimer inhibitor, broadly inhibits BRAF class I, II, III, BRAF fusions, and RAS-driven solid tumors leading to tumor regression in preclinical models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4045.

Abstract 1640: DP-9024, an investigational small molecule modulator of the Integrated Stress Response kinase PERK, causes B-cell cancer growth inhibition as single agent and in combination with standard-of-care agents

Background: The Integrated Stress Response (ISR) is a major adaptive stress response pathway in cancer cell maintenance. The ISR kinase family member PERK controls one of the three arms of the Unfolded Protein Response (UPR). The UPR is considered an Achilles’ heel in B-cell cancers. Multiple myeloma (MM) and B-cell lymphomas are dependent on a well-balanced UPR pathway to cope with the high demand for protein folding and their secretory nature. Given the double-edge sword nature of the UPR, the activation of PERK and downstream pathway can have cytoprotective or cytotoxic effects. In B-cell cancers the UPR is at close to maximum cytoprotective capacity, such that further pharmacological stimulation of PERK can potentially be leveraged to cause a cancer cell cytotoxic response and induce antitumoral effects.

Methods: Modulation of ISR kinases was characterized using enzymatic assays. Kinome selectivity profiling was determined using enzymatic and cellular assays. Cellular assays of PERK activation assessed ATF4 by ELISA. Cellular assays of GCN2 modulation assessed phospho-GCN2 and ATF4 by Western blot or ELISA (under basal or low amino acid conditions). DP-9024-induced upregulation of components of the ISR/UPR pathway (ATF4, CHOP) or the apoptosis pathway (PARP and Caspase 3/7) was measured by Western blot or ELISA assays. Compound-mediated PERK activation was investigated mechanistically using a cellular nanoBRET dimerization assay. In vivo upregulation of tumoral ATF4 was determined in a MM PK/PD xenograft model. In vivo inhibition of tumor growth was determined in MM and B-cell lymphoma xenografts.

Results: DP-9024 was designed as a selective and potent modulator of PERK and GCN2. DP-9024 was found to upregulate the ISR/UPR pathway (ATF4, CHOP). The mechanism by which DP-9024 treatment induced the UPR pathway was found to be through the dimerization and activation of PERK. Upregulation of the UPR pathway downstream of PERK led to induction of apoptosis (PARP and Caspase 3/7) in MM and B-cell lymphoma lines in vitro. DP-9024 mediated activation of the UPR pathway in cell lines with high basal level of endoplasmic reticulum (ER) stress led to growth arrest in combination with FDA approved therapies. Oral dosing of DP-9024 in MM xenograft models induced ATF4, and combination efficacy was observed in MM and B-cell lymphoma xenografts in combination with FDA approved agents in vivo.

Conclusions: The ISR/UPR is a targetable vulnerability in cancers with high basal levels of ER stress. DP-9024 increases UPR signaling via activating PERK dimerization. This novel mechanism leads to antitumoral effects in B-cell cancers in vitro and in vivo likely through the induction of unresolved ER stress, which may potentially provide an alternative mechanism to current UPR targeting therapies.

Citation Format: Gada Al-Ani, Qi Groer, Aaron J. Rudeen, Kristin M. Elliott, Patrick C. Kearney, Jeffery D. Zwicker, Yu Mi Ahn, Stacie L. Bulfer, Cale L. Heiniger, Molly M. Hood, Salim Javed, Joshua W. Large, Max D. Petty, Kristen L. Stoltz, Bertrand Le Bourdonnec, Bryan D. Smith, Daniel L. Flynn. DP-9024, an investigational small molecule modulator of the Integrated Stress Response kinase PERK, causes B-cell cancer growth inhibition as single agent and in combination with standard-of-care agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1640.

Abstract 4872: DCC-3116, a first-in-class selective ULK1/2 inhibitor of autophagy, in combination with the KIT inhibitor ripretinib induces complete regressions in GIST preclinical models

Background: Cancer cells activate autophagy as an adaptive stress response (ASR) mechanism to therapies targeting the RTK/RAS/MAPK/PI3K pathways, limiting antitumor response. Autophagy is initiated through ULK1/2 kinases and is triggered by inhibitors of the MAPK and PI3K pathways. Most gastrointestinal stromal tumors (GIST) are driven by mutations in KIT kinase. KIT signals through MAPK/PI3K pathways, suppressing ULK1/2 kinases and autophagy1,2,3. Inhibition of mutant KIT reverses this suppression, activating autophagy and cancer cell survival. Approved therapies for GIST include imatinib, sunitinib, regorafenib, ripretinib, and avapritinib. Treatment with these inhibitors is initially successful, but drug resistance can develop either through KIT secondary mutations or ASR pathways including autophagy. DCC-3116 is a selective, potent, first-in-class investigational inhibitor of the ULK1/2 in clinical development in combination with targeted therapies that activate the autophagic ASR pathway. Herein we demonstrate that ULK1/2 and autophagy are activated upon treatment with ripretinib in KIT mutant GIST models

A combination of ripretinib with DCC-3116 inhibits autophagy in vitro and leads to complete tumor regressions in preclinical models of GIST.

Methods: Inhibition of ULK1/2 in cell assays was measured using an ELISA for the ULK substrate phospho-ATG13 (pATG13). Autophagic flux was measured by monitoring mCherry/GFP tagged LC3 protein in GIST cells. Xenograft studies were performed at CROs.

Results: Ripretinib treatment led to the activation of ULK1/2 by 2-3-fold in mutant KIT GIST cell lines. DCC-3116 inhibited both ripretinib-induced and basal pATG13 with IC50 values of 12-32 nM. Treatment of GIST-T1 cells with ripretinib increased autophagic flux 3-fold. DCC-3116 potently inhibited flux with an IC50 value of 38 nM. Ripretinib also induced pATG13 and autophagic flux (1.5-2.5-fold) in multiple imatinib-resistant cell lines, which was inhibited by DCC-3116 with IC50 values between 8-189 nM. In a GIST T1 PK/PD model, DCC-3116 inhibited ULK1/2-mediated pATG13. The combination of DCC-3116 with ripretinib resulted in complete tumor regressions in comparison to single agent treatment in GIST preclinical models.

Conclusions: These data demonstrate preclinically that, like other receptor tyrosine kinase inhibitors1, ripretinib activates ULK1/2-mediated autophagy as an ASR resistance mechanism which is inhibited by DCC-3116, providing the rationale to study the combination of DCC-3116 with ripretinib in GIST patients. DCC-3116 is currently in a Phase 1 clinical trial in patients with advanced solid tumors (NCT04892017).

References: 1. Bogdan et al. 2021. Mol Cancer Ther 20(12 Suppl):Abstract P084. 2. Gupta et al. 2010. PNAS 107:14333-83.Li et al. 2013. Lung Cancer 81:354-61

Citation Format: Madhumita Bogdan, Mary J. Timson, Hikmat Al-Hashimi, Bryan D. Smith, Daniel L. Flynn. DCC-3116, a first-in-class selective ULK1/2 inhibitor of autophagy, in combination with the KIT inhibitor ripretinib induces complete regressions in GIST preclinical models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4872.

Abstract 1613: Dimerization-induced activation of the integrated stress response kinase PERK by an investigational small molecule modulator, DP-9024

Background: The Integrated Stress Response (ISR) is a major adaptive stress response pathway in cancers. The ISR kinase family member PERK controls one of the three arms of the Unfolded Protein Response (UPR). The UPR is considered an Achilles’ heel in B-cell cancers. Myelomas and B-cell lymphomas are dependent on a well-balanced UPR pathway to cope with the high demand for protein folding and their secretory nature. Given the double-edge sword nature of the UPR, the activation of PERK and downstream pathway can have cytoprotective or cytotoxic effects. In B-cell cancers the UPR is at close to maximum cytoprotective capacity, such that further pharmacological stimulation of PERK drives a cytotoxic outcome leveraged to induce antitumoral effects. Methods: Recombinant WT and mutant PERK constructs were assayed in the presence of DP-9024. Structures of compound-bound PERK were determined by X-ray crystallography. Kinome profiling was determined using enzymatic and cellular assays. Cellular modulation of the ISR/UPR pathway (phospho-GCN2, PERK, ATF4, CHOP) or the apoptosis pathway (cleaved-PARP, cleaved-Caspase 3/7) was measured by Western blot or ELISA. The level of DP-9024-induced PERK activation was determined using a cellular nanoBRET dimerization assay utilizing WT and mutant PERK constructs. Results: DP-9024 was designed as a selective and potent modulator of PERK and GCN2. DP-9024 was found to upregulate the ISR/UPR pathway (ATF4, CHOP). The mechanism by which DP-9024 induced the UPR pathway was found to be through dimerization-dependent activation of PERK. Utilizing recombinant biophysical and cellular assays of WT and mutant PERK constructs, we found that DP-9024 directly binds to a switch control site in the kinase domain of PERK that governs dimerization and that the binding of the compound to one monomer was sufficient to induce dimerization-mediated activation of the unoccupied monomer. This paradoxical stimulation of the unbound PERK monomer is reminiscent of the phenomenon observed with some BRAF inhibitors.1 X-ray crystallography studies revealed that PERK crystalizes as a dimer with both monomers bound to compound, due to the high concentration of compound used during crystallization. DP-9024-mediated PERK dimerization and transactivation led to the activation of downstream pathways (ATF4, CHOP), apoptotic pathway (Caspase 3/7, PARP1), and growth arrest in cell lines with high levels of endoplasmic reticulum (ER) stress such as multiple myeloma and B-cell lymphoma. Conclusions: Paradoxical stimulation of the ISR family member kinase PERK, through direct binding and dimerization by DP-9024, led to unresolved ER stress that can potentially be leveraged as a novel mechanism to induce growth arrest in UPR vulnerable cancers, including myelomas and B-cell lymphomas. References: 1. Poulikakos et al. 2010. Nature 464:427-30

Citation Format: Gada Al-Ani, Aaron J. Rudeen, Qi Groer, Kristin M. Elliott, Patrick C. Kearney, Jeffery D. Zwicker, Yu Mi Ahn, Stacie L. Bulfer, Cale L. Heiniger, Molly M. Hood, Salim Javid, Joshua W. Large, Max D. Petty, Kristen L. Stoltz, Bertrand Le Bourdonnec, Bryan D. Smith, Daniel L. Flynn. Dimerization-induced activation of the integrated stress response kinase PERK by an investigational small molecule modulator, DP-9024 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1613.

Discovery of vimseltinib (DCC-3014), a highly selective CSF1R switch-control kinase inhibitor, in clinical development for the treatment of Tenosynovial Giant Cell Tumor (TGCT)

Based on knowledge of kinase switch-control inhibition and using a combination of structure-based drug design and standard medicinal chemistry principles, we identified a novel series of dihydropyrimidone-based CSF1R kinase inhibitors displaying exquisite selectivity for CSF1R versus a large panel of kinases and non-kinase protein targets. Starting with lead compound 3, an SAR optimization campaign led to the discovery of vimseltinib (DCC-3014; compound 20) currently undergoing clinical evaluation for the treatment of Tenosynovial Giant Cell Tumor (TGCT), a locally aggressive benign tumor associated with substantial morbidity. 2021 Elsevier ltd. All rights reserved.

Discovery of acyl ureas as highly selective small molecule CSF1R kinase inhibitors

Based on the structure of an early lead identified in Deciphera's proprietary compound collection of switch control kinase inhibitors and using a combination of medicinal chemistry guided structure activity relationships and structure-based drug design, a novel series of potent acyl urea-based CSF1R inhibitors was identified displaying high selectivity for CSF1R versus the other members of the Type III receptor tyrosine kinase (RTK) family members (KIT, PDGFR-α, PDGFR-β, and FLT3), VEGFR2 and MET. Based on in vitro biology, in vitro ADME and in vivo PK/PD studies, compound 10 was selected as an advanced lead for Deciphera's CSF1R research program.

Abstract 3600: DCC-3116, a first-in-class selective inhibitor of ULK1/2 kinases and autophagy, synergizes with the KRASG12C inhibitor sotorasib resulting in tumor regression in KRAS mutant NSCLC xenograft models

Mutationally-activated RAS oncoproteins are detected in approximately 19% of newly diagnosed human cancers and have been targets for drug discovery for over 40 years. Recently, the FDA approved sotorasib, a covalent inhibitor of KRASG12C, for the treatment of non-small cell lung cancer (NSCLC). Although sotorasib demonstrated clear clinical benefits, the emergence of drug resistance has led to drug combination approaches with the goal of deepening and sustaining the durability of patient responses. One potential mechanism of drug resistance is the induction of autophagy, which cancer cells use to survive during periods of stress such as treatment with pathway-targeted therapies. Indeed, KRAS-mutated cancer cells have been shown to exhibit constitutive autophagy for survival. Additionally, such cells further increase autophagy when treated with pathway-targeted inhibitors of RAS>RAF>MEK>ERK MAP kinase signaling as a resistance mechanism. Hence, the combination of a KRASG12C inhibitor with a specific and potent autophagy inhibitor could lead to deeper and more sustained clinical responses. DCC-3116 is an investigational, potent and selective pharmacological inhibitor of the protein kinases ULK1 and ULK2, which are critical initiating components of the autophagy pathway. Treatment of KRASG12C non-small cell lung cancer (NSCLC) cell lines with sotorasib induced autophagy by ~2-fold via activation of ULK kinases as measured by an increase in ULK-mediated phosphorylation of ATG13. Sotorasib-mediated ULK kinase activation, and resulting autophagic flux, was inhibited by DCC-3116 in a dose-dependent manner with IC50 values of 81-160 nM in NSCLC cell lines. These effects translated to in vivo efficacy. In the Calu-1 and H358 KRASG12C NSCLC xenograft models, the combination of DCC-3116 and sotorasib resulted in tumor regression whereas single treatment arms afforded only inhibition of tumor growth. A NSCLC KRASG12C patient derived xenograft (PDX) model further supported the DCC-3116 and sotorasib combination with increased tumor growth inhibition compared to sotorasib alone. These data demonstrate a compelling rationale to study DCC-3116 in combination with KRASG12C inhibitors such as sotorasib in NSCLC patients. DCC-3116 is currently in a Phase 1 clinical trial in patients with advanced solid tumors with documented KRAS, NRAS or BRAF mutations (NCT04892017).

Citation Format: Martin McMahon, Madhumita Bogdan, Mary J. Timson, Hikmat Al-Hashimi, Phaedra Ghazi, Yu Zhan, Bryan D. Smith, Conan G. Kinsey, Daniel L. Flynn. DCC-3116, a first-in-class selective inhibitor of ULK1/2 kinases and autophagy, synergizes with the KRASG12C inhibitor sotorasib resulting in tumor regression in KRAS mutant NSCLC xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3600.

Abstract P084: DCC-3116, a first-in-class selective inhibitor of ULK1/2 kinases and autophagy, synergizes with EGFR inhibitors osimertinib and afatinib in NSCLC preclinical models

Background: Activating mutations in EGFR have been reported in ~30% of patients with non-small cell lung cancer (NSCLC). Three generations of small molecule EGFR kinase inhibitors have been approved by the FDA to treat these patients, however, multiple mechanisms of resistance cause cancer progression. In addition to drug-resistant mutations that arise and re-activate EGFR, other signaling pathways can be activated to cause resistance. Although EGFR inhibitors such as osimertinib and afatinib (also a pan-ErbB inhibitor) have demonstrated clear clinical benefits, patients inevitably develop resistance. Herein we demonstrate mutant EGFR NSCLCs activate autophagy upon treatment with EGFR inhibitors as a drug resistance mechanism. Therefore, a combination of an EGFR inhibitor with an autophagy inhibitor has the potential to deepen and prolong responses and improve patient outcomes. Materials and Methods: Human cancer cells with EGFR mutations were cultured using recommended complete medium. Inhibition of ULK1/2 was measured through standard biochemical assays and cellular readouts including NanoBRET and ELISA-based ATG13 phosphorylation assays. Autophagosome formation was measured using the CytoID assay (Enzo Life Sciences). For in vivo studies, NCI-H1975 cells that harbor an EGFR T790M resistance mutation were inoculated into BALB/c nude mice. Statistical analyses for the in vivo studies were performed using the Student’s t-test. Results: Erlotinib, gefitinib, osimertinib, and afatinib activated autophagy 3–4-fold over basal levels in the HCC827 cell line (EGFR exon 19 deletion) as measured by increases in phosphorylated ATG13, a cellular substrate of the autophagy-initiating kinases ULK1/2. DCC-3116, an investigational potent and selective dual inhibitor of ULK1 (IC50 6 nM) and ULK2 (9 nM) in cellular assays, inhibited both EGFR-induced and basal phosphorylation of ATG13 with IC50 values of 61–66 nM. Treatment of the NCI-H1975 EGFR mutated (L858R/T790M) NSCLC cell line with osimertinib or afatinib induced autophagy 3-fold over basal levels. DCC-3116 potently inhibited osimertinib and afatinib induced phosphorylation of ATG13 with IC50 values of 91 nM and 71 nM, respectively, and inhibited the increase in autophagosomes induced by these agents. Importantly, these in vitro effects translated to in vivo efficacy. The combination of DCC-3116 with osimertinib or afatinib resulted in significantly greater tumor responses than single agent treatments in the NCI-H1975 NSCLC xenograft model (combination vs. osimertinib p = 0.0005; combination vs. afatinib p = 0.0001; osimertinib combination vs vehicle p < 0.0001; afatinib combination vs. vehicle p < 0.0001). These data provide a strong rationale to study the combination of the ULK inhibitor DCC-3116 with EGFR inhibitors such as osimertinib and afatinib in cancer patients. DCC-3116 is currently in a Phase 1 clinical trial in patients with advanced solid tumors with a documented RAS or RAF mutation (NCT04892017).

Citation Format: Madhumita Bogdan, Mary J. Timson, Hikmat Al-Hashimi, Yu Zhan, Bryan D. Smith, Daniel L. Flynn. DCC-3116, a first-in-class selective inhibitor of ULK1/2 kinases and autophagy, synergizes with EGFR inhibitors osimertinib and afatinib in NSCLC preclinical models [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P084.

Vimseltinib: A Precision CSF1R Therapy for Tenosynovial Giant Cell Tumors and Diseases Promoted by Macrophages

Macrophages can be co-opted to contribute to neoplastic, neurologic, and inflammatory diseases. Colony-stimulating factor 1 receptor (CSF1R)-dependent macrophages and other inflammatory cells can suppress the adaptive immune system in cancer and contribute to angiogenesis, tumor growth, and metastasis. CSF1R-expressing osteoclasts mediate bone degradation in osteolytic cancers and cancers that metastasize to bone. In the rare disease tenosynovial giant cell tumor (TGCT), aberrant CSF1 expression and production driven by a gene translocation leads to the recruitment and growth of tumors formed by CSF1R-dependent inflammatory cells. Small molecules and antibodies targeting the CSF1/CSF1R axis have shown promise in the treatment of TGCT and cancer, with pexidartinib recently receiving FDA approval for treatment of TGCT. Many small-molecule kinase inhibitors of CSF1R also inhibit the closely related kinases KIT, PDGFRA, PDGFRB, and FLT3, thus CSF1R suppression may be limited by off-target activity and associated adverse events. Vimseltinib (DCC-3014) is an oral, switch control tyrosine kinase inhibitor specifically designed to selectively and potently inhibit CSF1R by exploiting unique features of the switch control region that regulates kinase conformational activation. In preclinical studies, vimseltinib durably suppressed CSF1R activity in vitro and in vivo, depleted macrophages and other CSF1R-dependent cells, and resulted in inhibition of tumor growth and bone degradation in mouse cancer models. Translationally, in a phase I clinical study, vimseltinib treatment led to modulation of biomarkers of CSF1R inhibition and reduction in tumor burden in TGCT patients.

Ripretinib and MEK Inhibitors Synergize to Induce Apoptosis in Preclinical Models of GIST and Systemic Mastocytosis

The majority of gastrointestinal stromal tumors (GIST) harbor constitutively activating mutations in KIT tyrosine kinase. Imatinib, sunitinib, and regorafenib are available as first-, second-, and third-line targeted therapies, respectively, for metastatic or unresectable KIT-driven GIST. Treatment of patients with GIST with KIT kinase inhibitors generally leads to a partial response or stable disease but most patients eventually progress by developing secondary resistance mutations in KIT. Tumor heterogeneity for secondary resistant KIT mutations within the same patient adds further complexity to GIST treatment. Several other mechanisms converge and reactivate the MAPK pathway upon KIT/PDGFRA-targeted inhibition, generating treatment adaptation and impairing cytotoxicity. To address the multiple potential pathways of drug resistance in GIST, the KIT/PDGFRA inhibitor ripretinib was combined with MEK inhibitors in cell lines and mouse models. Ripretinib potently inhibits a broad spectrum of primary and drug-resistant KIT/PDGFRA mutants and is approved by the FDA for the treatment of adult patients with advanced GIST who have received previous treatment with 3 or more kinase inhibitors, including imatinib. Here we show that ripretinib treatment in combination with MEK inhibitors is effective at inducing and enhancing the apoptotic response and preventing growth of resistant colonies in both imatinib-sensitive and -resistant GIST cell lines, even after long-term removal of drugs. The effect was also observed in systemic mastocytosis (SM) cells, wherein the primary drug-resistant KIT D816V is the driver mutation. Our results show that the combination of KIT and MEK inhibition has the potential to induce cytocidal responses in GIST and SM cells.

A Phase I Study of LY3009120, a Pan-RAF Inhibitor, in Patients with Advanced or Metastatic Cancer

Mutations in ERK signaling drive a significant percentage of malignancies. LY3009120, a pan-RAF and dimer inhibitor, has preclinical activity in RAS- and BRAF-mutated cell lines including BRAF-mutant melanoma resistant to BRAF inhibitors. This multicenter, open-label, phase I clinical trial (NCT02014116) consisted of part A (dose escalation) and part B (dose confirmation) in patients with advanced/metastatic cancer. In part A, oral LY3009120 was dose escalated from 50 to 700 mg twice a day on a 28-day cycle. In part B, 300 mg LY3009120 was given twice a day. The primary objective was to identify a recommended phase II dose (RP2D). Secondary objectives were to evaluate safety, pharmacokinetics, and preliminary efficacy. Identification of pharmacodynamic biomarkers was exploratory. In parts A and B, 35 and 16 patients were treated, respectively (N = 51). In part A, 6 patients experienced eight dose-limiting toxicities. The RP2D was 300 mg twice a day. Common (>10%) any-grade drug-related treatment-emergent adverse events were fatigue (n = 15), nausea (n = 12), dermatitis acneiform (n = 10), decreased appetite (n = 7), and maculopapular rash (n = 7). The median duration of treatment was 4 weeks; 84% of patients completed one or two cycles of treatment. Exposures observed at 300 mg twice a day were above the preclinical concentration associated with tumor regression. Eight patients had a best overall response of stable disease; there were no complete or partial clinical responses. Despite adequate plasma exposure levels, predicted pharmacodynamic effects were not observed.

Abstract B129: Preclinical studies with DCC-3116, an ULK kinase inhibitor designed to inhibit autophagy as a potential strategy to address mutant RAS cancers

Background: Cancer cells activate autophagy, a catabolic process to resupply nutrients and recycle damaged organelles, in order to survive stresses such as limited nutrients and hypoxia, or chemotherapy treatments. RAS mutant cancers, in particular, have been found to require autophagy for tumor growth and survival.1,2 Treating RAS mutant tumors with inhibitors of the downstream MAPK pathway has been largely unsuccessful, as these drugs have been shown to further stimulate autophagy, allowing for tumor cell survival.3,4 Inhibiting autophagy in combination with MAPK pathway inhibition may represent a possible new treatment paradigm for RAS mutant cancers. Proof-of-concept for this strategy was obtained in cancer models and in a RAS mutant pancreatic cancer patient by blocking autophagy with derivatives of chloroquine, in combination with MAPK inhibitors.3,4 Chloroquines indirectly block autophagy via disruption of lysosomal function, which may also affect important normal cellular processes. Chloroquines accumulate in tissues, notably the brain, where autophagy may be vital for neuronal health. The potential exists to more selectively inhibit autophagy by targeting specific components of the autophagy pathway. ULK1/2 kinases initiate autophagy and provide the potential for a targeted approach for selectively inhibiting autophagy in RAS mutant cancers. Herein, we describe preclinical studies with the ULK inhibitor DCC-3116, designed as a potential inhibitor of autophagy in RAS mutant cancers. Methods: In vitro kinase assays were performed using cellular levels of ATP (1 mM) and a peptide substrate. In cell assays, ULK activity was assessed using an ELISA for phosphorylated ATG13. Autophagosome formation was measured using the dye, Cyto-ID. Autophagic flux was assessed using cells expressing the autophagy protein LC3 fused to luciferase. The synergy of DCC-3116 in combination with MAPK inhibitors was assessed in 2D or 3D cell growth assays. Xenograft models were used to assess pharmacokinetics (PK) and pharmacodynamics (PD), as well as efficacy in vivo. Results: DCC-3116 is a potent and selective inhibitor of ULK1/2, inhibiting no other kinases within 30-fold of ULK potency, and only 5 kinases within 100-fold. DCC-3116 inhibited phosphorylation of the ULK substrate ATG13 in cancer cell assays. DCC-3116 inhibited autophagosome formation, as well as degradation of the autophagy marker LC3. DCC-3116 exhibited synergy in vitro in combination with MAPK pathway inhibitors in inhibiting cancer cell growth. In PK/PD models, oral doses of DCC-3116 led to sustained inhibition of ATG13 phosphorylation. DCC-3116, in combination with MAPK inhibitors, exhibited additivity or synergy in inhibiting tumor growth in xenograft models. DCC-3116 exhibited low brain penetration in rats, minimizing inhibition of CNS autophagy. Conclusion: Selectively blocking autophagy via inhibition of ULK kinases, in combination with MAPK pathway inhibition, is a promising therapeutic approach for RAS mutant cancers. DCC-3116 warrants further study as an inhibitor of autophagy, and has been selected as a candidate for potential development in the treatment of RAS mutant cancers.

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Citation Format: Bryan D Smith, Lakshminarayana Vogeti, Anu Gupta, Jarnail Singh, Gada Al-Ani, Stacie L Bulfer, Timothy M Caldwell, Mary J Timson, Subha Vogeti, Yu Mi Ahn, Hikmat Al-Hashimi, Chase K Crawley, Cale L Heiniger, Cynthia B Leary, Justin T Proto, Quanrong Shen, Hanumaiah Telikepalli, Karen Yates, Wei-Ping Lu, Daniel L Flynn. Preclinical studies with DCC-3116, an ULK kinase inhibitor designed to inhibit autophagy as a potential strategy to address mutant RAS cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B129. doi:10.1158/1535-7163.TARG-19-B129

Ripretinib (DCC-2618) Is a Switch Control Kinase Inhibitor of a Broad Spectrum of Oncogenic and Drug-Resistant KIT and PDGFRA Variants

Ripretinib (DCC-2618) was designed to inhibit the full spectrum of mutant KIT and PDGFRA kinases found in cancers and myeloproliferative neoplasms, particularly in gastrointestinal stromal tumors (GISTs), in which the heterogeneity of drug-resistant KIT mutations is a major challenge. Ripretinib is a "switch-control" kinase inhibitor that forces the activation loop (or activation "switch") into an inactive conformation. Ripretinib inhibits all tested KIT and PDGFRA mutants, and notably is a type II kinase inhibitor demonstrated to broadly inhibit activation loop mutations in KIT and PDGFRA, previously thought only achievable with type I inhibitors. Ripretinib shows efficacy in preclinical cancer models, and preliminary clinical data provide proof-of-concept that ripretinib inhibits a wide range of KIT mutants in patients with drug-resistant GISTs.

Abstract 3925: Inhibition of oncogenic and drug-resistant PDGFRA and KIT alterations by DCC-2618

Introduction:

Activating mutations and other genetic alterations in KIT and PDGFRA receptor tyrosine kinases have been identified in certain cancers and proliferative diseases, including most cases of gastrointestinal stromal tumors (GIST) and systemic mastocytosis, and small percentages of gliomas, lung cancer, and leukemias. The treatment of metastatic GIST has been transformed with KIT inhibitors, but heterogeneous drug-resistant mutations arise during therapy, with individual patients often having multiple KIT mutations in different tumor sites. PDGFRA variants in GIST and other cancers also have a significant unmet medical need. DCC-2618 is a kinase switch control inhibitor that potently inhibits the spectrum of exon 9, 11, 13, 14, 17 and 18 mutations in KIT and exons 12, 14 and 18 mutations in PDGFRA. DCC-2618 has been designed to bind as a type II kinase inhibitor that forces the mutant kinases, including strongly activated mutants such as D816V KIT and D842V PDGFRA, into inactive conformations. DCC-2618 has been observed to be potent in enzyme and cell-based assays, and has demonstrated consistent efficacy in xenograft models driven by PDGFRA and KIT alterations.

Methods:

DCC-2618, and an active human metabolite, DP-5439, were tested for inhibition of PDGFRA and KIT mutants using standard enzyme and binding assays, and a variety of cell-based assays. Levels of phosphorylated PDGFRA and KIT were determined by Western blot or ELISA. Proliferation was measured using the fluorescent dye resazurin. An x-ray crystal structure of an analog of DCC-2618 was determined at Emerald Biostructures. The H1703 PDGFRA-amplified lung cancer and GIST T1 mutant KIT xenograft models were performed at MI Bioresearch. A GIST PDX exon 17 mutant KIT xenograft model was run at Molecular Response.

Results:

DCC-2618 and the metabolite DP-5439 inhibited KIT and PDGFRA variants with nanomolar potency. In CHO cells transfected with KIT or PDGFRA variants, DCC-2618 was shown to inhibit the full spectrum of the clinically relevant primary and refractory drug-resistant mutations tested. DCC-2618 also inhibited phosphorylation of KIT or PDGFRA in cell lines with various drug-resistant KIT mutations or PDGFRA alterations. DCC-2618 was compared to the FDA-approved KIT inhibitors imatinib, sunitinib, regorafenib, and midostaurin, as well as other KIT and PDGFRA inhibitors.

In vivo, treatment with DCC-2618 led to tumor regressions in KIT- and PDGFRA-driven xenograft models.

Conclusions:

DCC-2618 has been observed to be a potent inhibitor of KIT and PDGFRA alterations, including mutants, fusions, and amplifications. Based on this profile, DCC-2618 may have utility in the treatment of KIT and PDGFRA-driven cancers including GIST, systemic mastocytosis, and a subset of lung cancers, gliomas, and leukemias. DCC-2618 is currently in a Phase 1 clinical trial in KIT and PDGFRA driven cancers (ClinicalTrials.gov Identifier: NCT02571036).

Citation Format: Bryan D. Smith, Michael D. Kaufman, Anu Gupta, Cynthia B. Leary, Wei-ping Lu, Stacie L. Bulfer, Gada Al-Ani, Jarnail Singh, Subha Vogeti, Michael C. Heinrich, Daniel L. Flynn. Inhibition of oncogenic and drug-resistant PDGFRA and KIT alterations by DCC-2618 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3925.

The Selective Tie2 Inhibitor Rebastinib Blocks Recruitment and Function of Tie2Hi Macrophages in Breast Cancer and Pancreatic Neuroendocrine Tumors

Tumor-infiltrating myeloid cells promote tumor progression by mediating angiogenesis, tumor cell intravasation, and metastasis, which can offset the effects of chemotherapy, radiation, and antiangiogenic therapy. Here, we show that the kinase switch control inhibitor rebastinib inhibits Tie2, a tyrosine kinase receptor expressed on endothelial cells and protumoral Tie2-expressing macrophages in mouse models of metastatic cancer. Rebastinib reduces tumor growth and metastasis in an orthotopic mouse model of metastatic mammary carcinoma through reduction of Tie2⁺ myeloid cell infiltration, antiangiogenic effects, and blockade of tumor cell intravasation mediated by perivascular Tie2^Hi/Vegf-A^Hi macrophages in the tumor microenvironment of metastasis (TMEM). The antitumor effects of rebastinib enhance the efficacy of microtubule inhibiting chemotherapeutic agents, either eribulin or paclitaxel, by reducing tumor volume, metastasis, and improving overall survival. Rebastinib inhibition of angiopoietin/Tie2 signaling impairs multiple pathways in tumor progression mediated by protumoral Tie2⁺ macrophages, including TMEM-dependent dissemination and angiopoietin/Tie2-dependent angiogenesis. Rebastinib is a promising therapy for achieving Tie2 inhibition in cancer patients. Mol Cancer Ther; 16(11); 2486-501. ©2017 AACR.

Phase 1 dose-finding study of rebastinib (DCC-2036) in patients with relapsed chronic myeloid leukemia and acute myeloid leukemia

A vailable tyrosine kinase inhibitors for chronic myeloid leukemia bind in an adenosine 5′-triphosphate-binding pocket and are affected by evolving mutations that confer resistance. Rebastinib was identified as a switch control inhibitor of BCR-ABL1 and FLT3 and may be active against resistant mutations. A Phase 1, first-in-human, single-agent study investigated rebastinib in relapsed or refractory chronic or acute myeloid leukemia. The primary objectives were to investigate the safety of rebastinib and establish the maximum tolerated dose and recommended Phase 2 dose. Fifty-seven patients received treatment with rebastinib. Sixteen patients were treated using powder-in-capsule preparations at doses from 57 mg to 1200 mg daily, and 41 received tablet preparations at doses of 100 mg to 400 mg daily. Dose-limiting toxicities were dysarthria, muscle weakness, and peripheral neuropathy. The maximum tolerated dose was 150 mg tablets administered twice daily. Rebastinib was rapidly absorbed. Bioavailability was 3- to 4-fold greater with formulated tablets compared to unformulated capsules. Eight complete hematologic responses were achieved in 40 evaluable chronic myeloid leukemia patients, 4 of which had a T315I mutation. None of the 5 patients with acute myeloid leukemia responded. Pharmacodynamic analysis showed inhibition of phosphorylation of substrates of BCR-ABL1 or FLT3 by rebastinib. Although clinical activity was observed, clinical benefit was insufficient to justify continued development in chronic or acute myeloid leukemia. Pharmacodynamic analyses suggest that other kinases inhibited by rebastinib, such as TIE2, may be more relevant targets for the clinical development of rebastinib (clinicaltrials.gov Identifier:00827138).

Abstract 4120: c-Met inhibition blocks MEK-induced tumor cell invasion in uveal melanoma

Uveal melanoma is the most common primary intraocular malignant tumor in adults. About half of patients with uveal melanoma will develop metastatic disease to the liver and the lung. These tumors are characterized by mutations in G-proteins (GNAQ and GNA11), activation of MAPK, and over-expression of c-Met. We have previously reported that c-Met inhibition inhibits tumor cell invasion and metastasis formation in uveal melanoma. Altiratinib is a selective inhibitor for c-Met as well as TIE2, VEGFR2 and TRK kinases. We found that this agent had no effect on inhibiting cell growth, consistent with our previous findings with crizotinib. However, it did inhibit invasion of uveal melanoma cells through matrigel in a concentration dependent fashion (25 nM to 250 nM) with inhibition of phospho-Met noted at concentrations as low as 25 nM. Selumetinib, a MEK inhibitor, is currently in clinical trial in patients with this disease. We found that treatment with 250 nM selumetinib inhibited cell proliferation but unexpectedly induced a marked increase in cell invasion of GNAQ and GNA11 mutant cell lines. This was associated with an increase in c-Met RNA and protein expression, as well as receptor phosphorylation, after 24 hours of selumetinib treatment. Combining selumetinib with altiratinib inhibited cell invasion to the level of altiratinib alone and continued to inhibit cell proliferation to the level of selumetinib alone. This effect was recapitulated by the knockdown of c-Met by siRNA prior to treatment with selumetinib. In a uveal melanoma xenograft model, the combination treatment of 15 mg/kg altiratinib and 25 mg/kg selumetinib significantly delayed tumor growth compared to vehicle control, altiratinib and selumetinib alone. Western blot analysis of tumor tissue confirmed target inhibition of p-Met and p-ERK in animals treated with altiratinib and selumetinib, respectively. Furthermore, tumor metastasis was inhibited by altiratinib, selumetinib and combination treatments in a uveal melanoma mouse model. These results indicate that the combined inhibition of MEK and c-Met by selumetinib and altiratinib, respectively, may be sufficient to suppress uveal melanoma tumor growth and metastasis. This strategy can potentially be used as therapy for patients with primary uveal melanoma who are at high risk for the development of metastatic disease.

Citation Format: Oliver Surriga, Bryan D. Smith, Grazia Ambrosini, Daniel L. Flynn, Richard D. Carvajal, Gary K. Schwartz. c-Met inhibition blocks MEK-induced tumor cell invasion in uveal melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4120.

Novel MET/TIE2/VEGFR2 inhibitor altiratinib inhibits tumor growth and invasiveness in bevacizumab-resistant glioblastoma mouse models

BACKGROUND

Glioblastoma highly expresses the proto-oncogene MET in the setting of resistance to bevacizumab. MET engagement by hepatocyte growth factor (HGF) results in receptor dimerization and autophosphorylation mediating tumor growth, invasion, and metastasis. Evasive revascularization and the recruitment of TIE2-expressing macrophages (TEMs) are also triggered by anti-VEGF therapy.

METHODS

We investigated the activity of altiratinib (a novel balanced inhibitor of MET/TIE2/VEGFR2) against human glioblastoma stem cell lines in vitro and in vivo using xenograft mouse models. The biological activity of altiratinib was assessed in vitro by testing the expression of HGF-stimulated MET phosphorylation as well as cell viability after altiratinib treatment. Tumor volume, stem cell and mesenchymal marker levels, microvessel density, and TIE2-expressing monocyte infiltration were evaluated in vivo following treatment with a control, bevacizumab alone, bevacizumab combined with altiratinib, or altiratinib alone.

RESULTS

In vitro, HGF-stimulated MET phosphorylation was completely suppressed by altiratinib in GSC17 and GSC267, and altiratinib markedly inhibited cell viability in several glioblastoma stem cell lines. More importantly, in multiple xenograft mouse models, altiratinib combined with bevacizumab dramatically reduced tumor volume, invasiveness, mesenchymal marker expression, microvessel density, and TIE2-expressing monocyte infiltration compared with bevacizumab alone. Furthermore, in the GSC17 xenograft model, altiratinib combined with bevacizumab significantly prolonged survival compared with bevacizumab alone.

CONCLUSIONS

Together, these data suggest that altiratinib may suppress tumor growth, invasiveness, angiogenesis, and myeloid cell infiltration in glioblastoma. Thus, altiratinib administered alone or in combination with bevacizumab may overcome resistance to bevacizumab and prolong survival in patients with glioblastoma.

Inhibition of RAF Isoforms and Active Dimers by LY3009120 Leads to Anti-tumor Activities in RAS or BRAF Mutant Cancers

LY3009120 is a pan-RAF and RAF dimer inhibitor that inhibits all RAF isoforms and occupies both protomers in RAF dimers. Biochemical and cellular analyses revealed that LY3009120 inhibits ARAF, BRAF, and CRAF isoforms with similar affinity, while vemurafenib or dabrafenib have little or modest CRAF activity compared to their BRAF activities. LY3009120 induces BRAF-CRAF dimerization but inhibits the phosphorylation of downstream MEK and ERK, suggesting that it effectively inhibits the kinase activity of BRAF-CRAF heterodimers. Further analyses demonstrated that LY3009120 also inhibits various forms of RAF dimers including BRAF or CRAF homodimers. Due to these unique properties, LY3009120 demonstrates minimal paradoxical activation, inhibits MEK1/2 phosphorylation, and exhibits anti-tumor activities across multiple models carrying KRAS, NRAS, or BRAF mutation.

Altiratinib Inhibits Tumor Growth, Invasion, Angiogenesis, and Microenvironment-Mediated Drug Resistance via Balanced Inhibition of MET, TIE2, and VEGFR2

Altiratinib (DCC-2701) was designed based on the rationale of engineering a single therapeutic agent able to address multiple hallmarks of cancer (1). Specifically, altiratinib inhibits not only mechanisms of tumor initiation and progression, but also drug resistance mechanisms in the tumor and microenvironment through balanced inhibition of MET, TIE2 (TEK), and VEGFR2 (KDR) kinases. This profile was achieved by optimizing binding into the switch control pocket of all three kinases, inducing type II inactive conformations. Altiratinib durably inhibits MET, both wild-type and mutated forms, in vitro and in vivo. Through its balanced inhibitory potency versus MET, TIE2, and VEGFR2, altiratinib provides an agent that inhibits three major evasive (re)vascularization and resistance pathways (HGF, ANG, and VEGF) and blocks tumor invasion and metastasis. Altiratinib exhibits properties amenable to oral administration and exhibits substantial blood-brain barrier penetration, an attribute of significance for eventual treatment of brain cancers and brain metastases.

Abstract 397: Rebastinib potently inhibits function of perivascular TIE2 expressing macrophages in vitro and in vivo

Introduction

Significant cross-talk between tumor cells and the surrounding stromal tissue are essential for tumor vascularization, survival, immunotolerance, invasion, and metastasis. The angiopoietin (ANG)/TIE2 kinase signaling pathway is a pivotal cross talk axis in the tumor microenvironment. It has been demonstrated that TIE2-expressing macrophages (TEMs) mediate invasion and metastasis in the PyMT syngeneic breast cancer model, and that TIE2 expression correlates with poor overall survival and high risk of metastasis in breast cancer patients. In this study, rebastinib was evaluated as a TIE2 inhibitor in in vitro and in vivo models, and was shown to have profound effects on the structure and function of perivascular TEMs.

Procedures

TIE2 kinase assays used a standard PK/LDH coupled spectrophotometric continuous assay. CHO cells were transiently transfected to express human TIE2 for cellular studies. CHOs, HUVECs and EA.hy926 cells were used to evaluate rebastinib for inhibition of ANG1-stimulated TIE2 phosphorylation. In vitro intravasation studies were performed in a transwell transendothelial migration chamber wherein TIE2HI macrophages interact with breast tumor cells to cause transendothelial migration of tumor cells across a sealed HUVEC endothelial monolayer. In vivo evaluations of rebastinib were performed using intravital high-resolution two-photon microscopy in the murine PyMT breast cancer model to evaluate effects on tumor vascular permeability and tumor cell intravasation.

Results

Rebastinib is a potent inhibitor of TIE2 kinase (IC50 = 0.63 nM). Rebastinib slowly dissociated from TIE2 (koff = 0.0012 minutes−1; T1/2 = 10 hr). In HUVECs or EA.hy926 cells, rebastinib inhibited ANG1-stimulated TIE2 kinase activity (IC50s of 0.018 and 0.091 nM, respectively). In TIE2 CHO cells, rebastinib inhibited TIE2 phosphorylation (IC50 2.0 nM), and demonstrated a prolonged off-rate (> 24 hr) against TIE2 after inhibitor washout. Rebastinib exhibited an IC50 < 5 nM for inhibiting macrophage-inducedbreast tumor cell intravasation in the in vitro transwell transendothelial migration assay.

Rebastinib was evaluated in vivo in the PyMT syngeneic breast cancer model. Rebastinib dosed at 10 mg/kg orally twice weekly impaired tumoral perivascular TEMs, resulting in a significant reduction in vascular permeability and in tumor cell intravasation as quantified by CTCs.

Conclusion Rebastinib is a potent inhibitor of TIE2 kinase and exhibits durable cellular inhibition in endothelial cells and in TIE2 macrophages. Oral dosing of rebastinib resulted in a significant reduction in TIE2-macrophage mediated tumor vascular permeability and in the intravasation of tumor cells into the circulation. Rebastinib is currently in Phase 1 clinical evaluation in solid tumors.

Citation Format: Allison Harney, Jeanine Pignatelli, Edison Leung, Maja Oktay, Yarong Wang, Bryan D. Smith, Daniel L. Flynn, John S. Condeelis. Rebastinib potently inhibits function of perivascular TIE2 expressing macrophages in vitro and in vivo. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 397. doi:10.1158/1538-7445.AM2015-397

Abstract 5125: Imaging the tumor microenvironment of metastasis reveals the mechanism of transient blood vessel permeability and tumor cell intravasation

Sites of direct contact between a macrophage, a tumor cell and endothelial cell [Tumor MicroEnvironment of Metastasis (TMEM)], correlates with metastasis in breast cancer patients independently of other clinical prognostic indicators suggesting a direct role for TMEM function in hematogenous dissemination. Here we show, using intravital high-resolution two-photon microscopy, that tumor cell intravasation occurs only at TMEM. Tumor cell intravasation occurs concurrently with transient, local vascular permeability at TMEM in an autochthonous mouse mammary carcinoma model and a human patient-derived xenograft model. Ablation of the presence or activity of the TMEM associated macrophages blocks tumor cell intravasation at TMEM demonstrating an essential role of perivascular macrophages in TMEM function. A subset of TMEM macrophages are identified as Tie2-expressing macrophages that are characterized by F4/80+/CD11b+/CD68+/MRC1+/Tie2Hi/VEGFAHi/CD11c-. VEGFA signaling from Tie2Hi TMEM-associated macrophages causes the local loss of vascular junctions resulting in transient vascular permeability and tumor cell intravasation at TMEM. Macrophage-specific ablation of VEGFA results in increased vascular junction stability and inhibition of intravasation, demonstrating that vascular junction dissolution at VEGFAHi/Tie2Hi TMEM-associated macrophages leads to vascular permeability and tumor cell intravasation. Inhibition of Tie2 with the first in class small molecular inhibitor rebastinib impairs TMEM function leading to a reduction in vascular permeability, tumor cell dissemination and metastasis. Further, rebastinib inhibition of Tie2 blocks tumor cell extravasation and metastatic growth in the lungs.

Together, the findings that TMEM macrophages mediate vascular permeability and tumor cell intravasation demonstrate an essential role for TMEM within the primary mammary tumor as sites of tumor cell dissemination. These data reveal the mechanism of tumor cell intravasation in breast cancer, explain the prognostic value of TMEM density in predicting distant metastatic recurrence in breast cancer patients and document a strategy for inhibition of dissemination.

This research is supported by the Department of Defense Breast Cancer Research Program under award number BC120227 (ASH), NIH CA100324 (JSC) and the Integrated Imaging Program.

Citation Format: Allison S. Harney, Esther N. Arwert, David Entenberg, Yarong Wang, Peng Guo, Bin-Zhi Qian, Bryan D. Smith, Jeffrey W. Pollard, Joan G. Jones, Daniel L. Flynn, John S. Condeelis. Imaging the tumor microenvironment of metastasis reveals the mechanism of transient blood vessel permeability and tumor cell intravasation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5125. doi:10.1158/1538-7445.AM2015-5125

Abstract 790: Altiratinib is a potent inhibitor of TRK kinases and is efficacious in TRK-fusion driven cancer models

Introduction:

TRK kinases have been implicated in a variety of cancers, wherein TRK gene fusions, amplifications and mutations have been shown to drive tumor growth. TRK kinases have also been shown to play key roles in metastasis. Recently, large-scale sequencing efforts have identified TRK fusions at a low but significant frequency across all major cancers. Altiratinib is a potent single-digit nanomolar inhibitor of TRK, MET, TIE2, and VEGFR2 kinases. Altiratinib inhibits TRKA, TRKB, and TRKC phosphorylation in both WT TRK and TRK-fusion cell lines and inhibits cell proliferation in these cell lines. In vivo, altiratinib suppressed TRK phosphorylation for >18 hr after a single oral dose and showed significant inhibition of tumor growth in TRKA and TRKC-fusion xenograft efficacy studies. Altiratinib is currently in a Phase 1 clinical trial for patients with advanced solid tumors.

Experimental procedures:

Altiratinib was tested for inhibition of various recombinant kinases using a standard PK/LDH coupled spectrophotometric continuous assay. In cell assays, cells were treated with a dose response of compound. Levels of phosphorylated TRK in cell lysates were determined Western blot. Cell proliferation was measured using the fluorescent dye resazurin. Experiments were performed in triplicate. In vivo xenograft models were performed at Molecular Imaging, Inc. (Ann Arbor, MI).

Summary of results:

Altiratinib potently inhibited TRK kinase activity in biochemical assays (IC50 values of 0.9 nM, 4.6 nM, and 0.8 nM for TRKA, B, and C, respectively). Altiratinib inhibited phosphorylation of TRKA in the TPM3-TRKA fusion cell line KM-12 (IC50 = 1.4 nM) and of TRKC in ETV6-TRKC transformed NIH-3T3 cells (IC50 = 0.5 nM). Altiratinib inhibited NGF-stimulated phosphorylation of wild-type TRKA in K562 (IC50 = 0.7 nM) and SK-N-SH cells (IC50 = 1.2 nM) and BDNF-stimulated phosphorylation of TRKB in ATRA-transformed SK-N-SH cells (IC50 = 0.24 nM). In compound washout experiments, altiratinib inhibited TRKA phosphorylation in KM-12 cells for > 24 hr after compound washout, due to its durable Type II switch pocket binding mode to the kinase. In cell lines driven by TRK fusions, altiratinib also inhibited cell proliferation (KM-12 IC50 = 3.8 nM; NIH-3T3 ETV6/TRKC IC50 = 0.5 nM). In vivo, altiratinib inhibited phosphorylation of TRK and downstream targets in the signaling pathway for >12 hr after a single oral dose. Altiratinib treatment led to tumor regression in TRK-fusion xenograft efficacy studies.

Conclusions:

Altiratinib exhibits potent inhibition of oncogenic TRK fusions in vitro and in vivo. Combined with its inhibition of the tumor and microenvironment targets MET, TIE2, and VEGFR2 kinases, altiratinib provides the potential to treat cancers driven by TRK fusions. Altiratinib is currently in a Phase 1 clinical trial in patients with solid tumors.

Citation Format: Bryan D. Smith, Cynthia B. Leary, Benjamin A. Turner, Michael D. Kaufman, Scott C. Wise, Maria E. R. Garcia-Rendueles, James A. Fagin, Daniel L. Flynn. Altiratinib is a potent inhibitor of TRK kinases and is efficacious in TRK-fusion driven cancer models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 790. doi:10.1158/1538-7445.AM2015-790

Discovery of 1-(3,3-dimethylbutyl)-3-(2-fluoro-4-methyl-5-(7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl)phenyl)urea (LY3009120) as a pan-RAF inhibitor with minimal paradoxical activation and activity against BRAF or RAS mutant tumor cells

The RAS-RAF-MEK-MAPK cascade is an essential signaling pathway, with activation typically mediated through cell surface receptors. The kinase inhibitors vemurafenib and dabrafenib, which target oncogenic BRAF V600E, have shown significant clinical efficacy in melanoma patients harboring this mutation. Because of paradoxical pathway activation, both agents were demonstrated to promote growth and metastasis of tumor cells with RAS mutations in preclinical models and are contraindicated for treatment of cancer patients with BRAF WT background, including patients with KRAS or NRAS mutations. In order to eliminate the issues associated with paradoxical MAPK pathway activation and to provide therapeutic benefit to patients with RAS mutant cancers, we sought to identify a compound not only active against BRAF V600E but also wild type BRAF and CRAF. On the basis of its superior in vitro and in vivo profile, compound 13 was selected for further development and is currently being evaluated in phase I clinical studies.

Abstract PR01: Rebastinib, a selective TIE2 kinase inhibitor, decreases TIE2-expressing macrophages, reduces metastasis, and increases survival in murine cancer models

In the tumor microenvironment, TIE2 expression on tissue macrophages, bone marrow derived TIE2-expressing monocytes (TEMs), osteoclasts, and vascular endothelial cells promotes tumor invasiveness, dissemination, and metastasis. Additionally, a subset of TIE2-expressing macrophages, located within specialized vascular structures known as tumor microenvironment for metastases (TMEMs), are linked to intravasation of cancer cells into circulation and dissemination to metastatic sites. Rebastinib is a picomolar inhibitor of TIE2 kinase, and exhibits an extraordinarily long off-rate from TIE2, measured to be over 24 hours in a cell-based assay. Herein, we examine the efficacy of rebastinib in the polyoma middle-T antigen (PyMT) syngeneic mouse breast cancer model. In this model, PyMT breast cancer cells are implanted in the mammary fat pad, and primary tumor growth leads to lung metastasis, which is known to be modulated by TEMs and TMEM vascular structures. We examined multiple dosing schedules of rebastinib in combination with anti-tubulin agents (ATAs). Rebastinib treatment in this model significantly ablated TEMs in the primary tumor stroma and caused a significant decrease in lung metastases. Furthermore, the combination of rebastinib with ATAs, even with once or twice weekly oral dosing of rebastinib, led to a significant further decrease in lung metastases compared to single-agent treatment with ATAs. Rebastinib also enhanced the activity of ATAs in reducing primary tumor growth and regrowth of tumor post-resection. TIE2 inhibition with targeted therapy represents a novel treatment approach for metastatic breast cancer and other cancers that rely on TEMs and TMEMs for growth and metastasis. As such, rebastinib has been selected for further clinical development in solid tumors with a Phase 1b trial being planned for 2014.

This abstract is also presented as Poster A5.

Citation Format: Daniel L. Flynn, Michael D. Kaufman, Cynthia B. Leary, Molly M. Hood, Wei-Ping Lu, Benjamin A. Turner, Scott C. Wise, Marc S. Rudoltz, Bryan D. Smith. Rebastinib, a selective TIE2 kinase inhibitor, decreases TIE2-expressing macrophages, reduces metastasis, and increases survival in murine cancer models. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr PR01. doi:10.1158/1538-7445.CHTME14-PR01

Abstract P4-15-12: Rebastinib in combination with eribulin ablates TIE2-expressing macrophages, reduces metastasis, and increases survival in the PyMT metastatic breast cancer model

In cancer models, TIE2 kinase plays an important role in angiogenesis, vasculogenesis, and tumor metastasis. TIE2 expression is largely restricted to vascular endothelial cells, tissue macrophages, and bone marrow derived TIE2-expressing monocytes (TEMs), which are proangiogenic, provasculogenic and enhance invasiveness. The hypoxic tumor environment engendered by damaging the vasculature with chemotherapy, radiation, or anti-angiogenic treatments leads to rebound tumor vascularization by an angiogenic switch from the VEGF pathway to the angiopoietin/TIE2 pathway. This leads to recruitment of provasculogenic TEMs from the bone marrow, leading to the growth of residual tumor cells and disease progression. Significantly, a subset of TIE2-expressing macrophages are located within specialized vascular structures known as tumor microenvironment for metastases (TMEMs). Recent observations have linked TIE2-expressing macrophages within TMEM structures to intravasation of cancer cells into circulation and subsequent dissemination to metastatic sites. We hypothesized that TIE2 inhibition should decrease migration and association of TEMs with blood vessels in the tumor stroma, therefore blocking their proangiogenic activity and leading to reduced tumor growth. TIE2 inhibition may also alter TMEM function, leading directly to a blockade of metastasis.

Rebastinib is a picomolar inhibitor of TIE2 kinase, and exhibits an extraordinarily long off-rate from TIE2, measured to be over 24 hours in a cell-based assay. Herein, we examine the efficacy of rebastinib in the polyoma middle-T antigen (PyMT) syngeneic mouse breast cancer model. In this model, PyMT breast cancer cells are implanted in the mammary fat pad, and primary tumor growth leads to metastasis, which is known to be modulated by TEMs and TMEM vascular structures. We examined dosing rebastinib in combination with eribulin, an inhibitor of microtubule dynamics that recently was FDA-approved for treatment-refractory metastatic breast cancer. Rebastinib treatment in this model significantly ablated TEMs in the primary tumor stroma and caused a significant decrease in lung metastases. Furthermore, the combination of rebastinib and eribulin led to a significant further decrease in lung metastases compared to treatment with eribulin alone (Table 1). Rebastinib also enhanced the activity of eribulin in reducing primary tumor growth and regrowth of tumor post-resection.

TIE2 inhibition represents a novel treatment approach for metastatic breast cancer and other cancers that rely on TEMs and TMEMs for growth and metastasis. As such, rebastinib has been selected for further clinical development in combination with eribulin for treatment-refractory metastatic breast cancer, with a Phase 1b trial being planned for late 2013.

Rebastinib reduces lung metastases in the PyMT breast cancer modelTreatmentLung Metastases (% of Control)Vehicle100%Eribulin 1 mg/kg three times/week71%Rebastinib 10 mg/kg twice/week + Eribulin 1 mg/kg23%Eribulin 0.3 mg/kg three times/week71%Rebastinib 10 mg/kg twice/week + Eribulin 0.3 mg/kg51%Eribulin 0.1 mg/kg three times/week72%Rebastinib 10 mg/kg twice/week + Eribulin 0.1 mg/kg43%

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-15-12.

Abstract P4-15-13: Rebastinib in combination with paclitaxel ablates TIE2-expressing macrophages, reduces metastasis, and increases survival in the PyMT metastatic breast cancer model

In cancer models, TIE2 kinase plays an important role in angiogenesis, vasculogenesis, and tumor metastasis. TIE2 expression is largely restricted to vascular endothelial cells, tissue macrophages, and bone marrow derived TIE2-expressing monocytes (TEMs), which are proangiogenic, provasculogenic and enhance invasiveness. The hypoxic tumor environment engendered by damaging the vasculature with chemotherapy, radiation, or anti-angiogenic treatments leads to rebound tumor vascularization by an angiogenic switch from the VEGF pathway to the angiopoietin/TIE2 pathway. This leads to recruitment of provasculogenic TEMs from the bone marrow, leading to the growth of residual tumor cells and disease progression. Significantly, a subset of TIE2-expressing macrophages are located within specialized vascular structures known as tumor microenvironment for metastases (TMEMs). Recent observations have linked TIE2-expressing macrophages within TMEM structures to intravasation of cancer cells into circulation and subsequent dissemination to metastatic sites. We hypothesized that TIE2 inhibition should decrease migration and association of TEMs with blood vessels in the tumor stroma, therefore blocking their proangiogenic activity and leading to reduced tumor growth. TIE2 inhibition may also alter TMEM function, leading directly to a blockade of metastasis.

Rebastinib is a picomolar inhibitor of TIE2 kinase, and exhibits an extraordinarily long off-rate from TIE2, measured to be over 24 hours in a cell-based assay. Herein, we examine the efficacy of rebastinib in the polyoma middle-T antigen (PyMT) syngeneic mouse breast cancer model. In this model, PyMT breast cancer cells are implanted in the mammary fat pad, and primary tumor growth leads to metastasis, which is known to be modulated by TEMs and TMEM vascular structures. We examined multiple dosing schedules of rebastinib in combination with paclitaxel. Rebastinib treatment in this model significantly ablated TEMs in the primary tumor stroma and caused a significant decrease in lung metastases (Table 1). Furthermore, the combination of rebastinib and paclitaxel led to a significant further decrease in lung metastases compared to treatment with paclitaxel or rebastinib alone. Rebastinib also enhanced the activity of paclitaxel in reducing primary tumor growth and regrowth of tumor post-resection.

TIE2 inhibition with targeted therapy represents a novel treatment approach for metastatic breast cancer and other cancers that rely on TEMs and TMEMs for growth and metastasis. As such, rebastinib has been selected for further clinical development for treatment-refractory metastatic breast cancer, with a Phase 1b trial being planned for late 2013.

Rebastinib reduces lung metastases in the PyMT breast cancer modelStudynTreatmentLung Metastases (% of Control)110Vehicle100%110Paclitaxel 10 mg/kg Q5D36%110Rebastinib 10 mg/kg BID28%110Rebastinib 10 mg/kg BID + Paclitaxel7%210Vehicle100%210Paclitaxel 10 mg/kg Q5D51%210Rebastinib 10 mg/kg QD + Paclitaxel21%33Vehicle100%33Paclitaxel 10 mg/kg Q5D58%33Rebastinib 10 mg/kg twice/week + Paclitaxel28%

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-15-13.

Abstract B78: Rebastinib, a small molecule TIE2 kinase inhibitor, prevents primary tumor growth and lung metastasis in the PyMT breast cancer model

Rebastinib is an inhibitor of tyrosine kinases TIE2 and ABL1. A clinical trial in chronic myeloid leukemia (CML) to inhibit BCR-ABL was previously performed but efficacy was modest and development in CML is not continuing. Rebastinib is approximately 50 times more potent as an inhibitor of TIE2 than BCR-ABL. Biomarker analysis of patients from the CML trial of rebastinib revealed that a majority displayed significant increases in circulating angiopoietin 2 (ANG2) levels. Increases in ANG2, a TIE2 ligand, have been previously reported to correlate with inhibition of the TIE2 pathway. The hypoxic tumor environment engendered by radiation therapy, cytotoxic chemotherapy, or anti-angiogenic treatments (such as anti-VEGF therapies) leads to rebound tumor vascularization by the recruitment of pro-vasculogenic TIE2 expressing monocytes (TEMs) from the bone marrow to these hypoxic tumor sites. TEMs are believed to play an important role in the revascularization of tumors after these treatments, leading to progression of residual tumor. Thus, inhibition of TEM recruitment and activity could lead to better patient outcomes.

The polyoma middle-T antigen (PyMT) syngeneic mouse breast cancer model utilizes the mouse mammary tumor virus (MMTV) promoter, a breast specific promoter, to express PyMT in mouse breast tissue. In this model, primary breast cancers spontaneously occur, proliferate, and metastasize (mainly to the lungs) and lead to the death of the mice. Unlike xenografts, the PyMT model utilizes fully immunocompetent mice and metastasis in this model is known to be modulated by TEMs. Rebastinib has been evaluated in a PyMT mouse where primary tumors were allowed to reach 800 mg in size before starting treatment. Rebastinib therapy resulted in a significant decrease in the growth rate of the primary breast tumor (75%), a 71% reduction in lung metastases, a decrease in the levels of tumoral TIE2 staining by immunohistochemical analysis (IHC) and caused the remaining tumor to become necrotic. Combining rebastinib with paclitaxel resulted in a synergistic response with 90% inhibition of tumor growth and a 93% reduction of lung metastases.

This presentation will focus on the biochemical, cellular and in vivo activity of rebastinib as a novel small molecule inhibitor of TIE2 kinase and its potential for prevention of primary tumor rebound and metastasis in combination with first line interventional therapy. A clinical trial exploring this activity is planned for 2013.

Citation Format: Bryan D. Smith, Molly M. Hood, Michael D. Kaufman, Mark Berger, Daniel L. Flynn, Scott C. Wise. Rebastinib, a small molecule TIE2 kinase inhibitor, prevents primary tumor growth and lung metastasis in the PyMT breast cancer model. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr B78.

Targeting the KIT activating switch control pocket: a novel mechanism to inhibit neoplastic mast cell proliferation and mast cell activation

Activating mutations in the receptor tyrosine kinase KIT, most notably KIT D816V, are commonly observed in patients with systemic mastocytosis. Thus, inhibition of KIT has been a major focus for treatment of this disorder. Here we investigated a novel approach to such inhibition. Utilizing rational drug design, we targeted the switch pocket (SP) of KIT which regulates its catalytic conformation. Two SP inhibitors thus identified, DP-2976 and DP-4851, were examined for effects on neoplastic mast cell proliferation and mast cell activation. Autophosphorylation of both wild type (WT) and, where also examined, KIT D816V was blocked by these compounds in transfected 293T cells, HMC 1.1 and 1.2 human mast cell lines; and in CD34⁺-derived human mast cells activated by stem cell factor (SCF). Both inhibitors induced apoptosis in the neoplastic mast cell lines and reduced survival of primary bone marrow mast cells from patients with mastocytosis. Moreover, the SP inhibitors more selectively blocked SCF potentiation of FcεRI-mediated degranulation. Overall, SP inhibitors represent an innovative mechanism of KIT inhibition whose dual suppression of KIT D816V neoplastic mast cell proliferation and SCF enhanced mast cell activation may provide significant therapeutic benefits.

The ABL switch control inhibitor DCC-2036 is active against the chronic myeloid leukemia mutant BCR-ABLT315I and exhibits a narrow resistance profile

Acquired point mutations within the BCR-ABL kinase domain represent a common mechanism of resistance to ABL inhibitor therapy in patients with chronic myeloid leukemia (CML). The BCR-ABL(T315I) mutant is highly resistant to imatinib, nilotinib, and dasatinib, and is frequently detected in relapsed patients. This critical gap in resistance coverage drove development of DCC-2036, an ABL inhibitor that binds the switch control pocket involved in conformational regulation of the kinase domain. We evaluated the efficacy of DCC-2036 against BCR-ABL(T315I) and other mutants in cellular and biochemical assays and conducted cell-based mutagenesis screens. DCC-2036 inhibited autophosphorylation of ABL and ABL(T315I) enzymes, and this activity was consistent with selective efficacy against Ba/F3 cells expressing BCR-ABL (IC(50): 19 nmol/L), BCR-ABL(T315I) (IC(50): 63 nmol/L), and most kinase domain mutants. Ex vivo exposure of CML cells from patients harboring BCR-ABL or BCR-ABL(T315I) to DCC-2036 revealed marked inhibition of colony formation and reduced phosphorylation of the direct BCR-ABL target CrkL. Cell-based mutagenesis screens identified a resistance profile for DCC-2036 centered around select P-loop mutations (G250E, Q252H, Y253H, E255K/V), although a concentration of 750 nmol/L DCC-2036 suppressed the emergence of all resistant clones. A decreased concentration of DCC-2036 (160 nmol/L) in dual combination with either nilotinib or dasatinib achieved the same zero outgrowth result. Further screens for resistance due to BCR-ABL compound mutations (two mutations in the same clone) identified BCR-ABL(E255V / T315I) as the most resistant mutant. Taken together, these findings support continued evaluation of DCC-2036 as an important new agent for treatment-refractory CML.

Abstract 3594: Conformational control of FMS kinase for treatment of human malignancies

FMS kinase is involved in the process of osteoclast maturation. Osteoclasts have been shown to play a role not only in arthritic diseases but also in a cancers ability to metastasize to the bone. This is especially true for breast, lung and prostate cancer. Taken together the ability to prevent osteoclast maturation and accumulation through FMS inhibition should be a good target for small molecule therapy of bone metastasis. Using Deciphera Pharmaceutical's approach to kinase inhibition, compounds have been designed that potently inhibit FMS kinase. These inhibitors can be highly selective with lead compounds inhibiting only a single kinase within 20 fold of FMS activity in a 300 kinase profile. A second class broadens the profile to include anti-angiogenic kinase targets in addition to potent FMS inhibition. This presentation will highlight the attributes and development status of these compounds for treatment of human malignancies.

Deciphera's FMS program has afforded potent inhibitors that achieve single digit nanomolar inhibition in biochemical assays of FMS activity. The inhibitors retain this same level of potency in the presence of high (5mM) ATP concentrations. These same compounds are also selective with some inhibiting as few as three kinases within 50 fold of FMS potency. In addition, proliferation and FMS phosphoprotein assays performed with M-NFS-60 and THP-1 cells have demonstrated excellent inhibitory profiles with achieved potencies in the low nanomolar range. In functional osteoclast differentiation models, key compounds have demonstrated single digit nanomolar inhibition as assessed by TRAP assays. In vivo evaluation of the inhibitors produced excellent tolerance in two week MTD studies. Potent and durable efficacy in pharmacokinetic/pharmacodynamic xenograft models was also observed demonstrating on target effects. In vivo models of bone invasion coupled with non-invasive translational image-based biomarkers potentially provide a powerful method for visualization and quantification of osteoclast activity and FMS inhibition. Early results in imaging of bone invasion will be presented using micro CT and fluorescent activateable probes.

Deciphera's FMS inhibitors show acceptable ADME properties in cell permeability, cytochrome p450 inhibition, microsomal clearance and are orally bioavailable in rat and dog. Key prototype compounds have been evaluated in a two week rat tolerability study. These data demonstrate that Deciphera's technology has been used to identify potent and selective FMS inhibitors to be developed for treatment of cancers where metastasis to bone is an issue.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3594. doi:10.1158/1538-7445.AM2011-3594

Conformational control inhibition of the BCR-ABL1 tyrosine kinase, including the gatekeeper T315I mutant, by the switch-control inhibitor DCC-2036

Acquired resistance to ABL1 tyrosine kinase inhibitors (TKIs) through ABL1 kinase domain mutations, particularly the gatekeeper mutant T315I, is a significant problem for patients with chronic myeloid leukemia (CML). Using structure-based drug design, we developed compounds that bind to residues (Arg386/Glu282) ABL1 uses to switch between inactive and active conformations. The lead "switch-control" inhibitor, DCC-2036, potently inhibits both unphosphorylated and phosphorylated ABL1 by inducing a type II inactive conformation, and retains efficacy against the majority of clinically relevant CML-resistance mutants, including T315I. DCC-2036 inhibits BCR-ABL1(T315I)-expressing cell lines, prolongs survival in mouse models of T315I mutant CML and B-lymphoblastic leukemia, and inhibits primary patient leukemia cells expressing T315I in vitro and in vivo, supporting its clinical development in TKI-resistant Ph(+) leukemia.

Monomer-on-monomer (MoM) Mitsunobu reaction: facile purification utilizing surface-initiated sequestration

A monomer-on-monomer (MoM) Mitsunobu reaction utilizing norbornenyl-tagged (Nb-tagged) reagents is reported, whereby purification was rapidly achieved by employing ring-opening metathesis polymerization, which was initiated by any of three methods utilizing Grubbs catalyst: (i) free catalyst in solution, (ii) surface-initiated catalyst-armed silica, or (iii) surface-initiated catalyst-armed Co/C magnetic nanoparticles.

Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region

Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.

Abstract LB-300: Small molecule modulators of MET kinase for treatment of human malignancies

MET kinase is involved in numerous cancers including lung, melanoma and gastric. MET can not only be the oncogenic driver of the cancer cell but also is a key player in the cells ability to metastasize and invade tissues distant from the primary tumor site. It has been shown that 2 out of 3 cancers involving MET leads to a poor prognosis for patient survival. Using Deciphera Pharmaceutical's approach to kinase inhibition, compounds have been designed which effectively inhibit wild type and mutant MET kinase forms. These inhibitors are selective, including sparing of close family members AXL and RON. This presentation will highlight the attributes and development status of these compounds for treatment of human malignancy. Deciphera's MET program has afforded potent inhibitors that achieve low nanomolar inhibition of wild type MET and secondary activating mutant forms. Data will be presented on DP-4693 and DP-4756.IC50MET Kinasep-MET MKN-45MKN-45 Proliferationp-MET EBC-1EBC-1 ProliferationA549 MigrationDP-46934nM13 nM44 nM10 nM3nM260 nMDP-47566nM6nM23 nM2nM5nM21 nM

DP-4693 and DP-4756 are selective, having as few as three kinases within 50 fold of MET potency. Inhibitor bound crystal structures will be shown which demonstrate the compounds mechanism of action. In addition, proliferation and MET phosphoprotein analysis performed with EBC-1 and MKN-45 cell lines have demonstrated excellent inhibitory profiles with potencies in the low nanomolar range. The compounds also inhibit HGF dependent cell motility in an A549 migration assay. In vivo evaluation of DP-4693 in an MKN-45 gastric cancer xenograft PK/PD model revealed complete target suppression at doses as low as 6 mpk. Futher studies will be presented highlighting the efficacy in both autocrine and paracrine (HGF-dependent) xenograft models.

Deciphera's MET inhibitors also show acceptable ADME properties and are orally bioavailable in rat and dog using simple vehicles. These inhibitors have also been evaluated in two week toxicology studies, exhibiting excellent tolerability up to doses of 300 mpk. Further studies are ongoing to enable Development Candidate selection for progression into clinical trials.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-300.

Identification of SD-0006, a potent diaryl pyrazole inhibitor of p38 MAP kinase

Starting from an initial HTS screening lead, a novel series of C(5)-substituted diaryl pyrazoles were developed that showed potent inhibition of p38alpha kinase. Key to this outcome was the switch from a pyridyl to pyrimidine at the C(4)-position leading to analogs that were potent in human whole blood based cell assay as well as in a number of animal efficacy models for rheumatoid arthritis. Ultimately, we identified a clinical candidate from this substrate; SD-0006.

High-load, oligomeric dichlorotriazine: a versatile ROMP-derived reagent and scavenger

A new high-load, soluble oligomeric dichlorotriazine (ODCT) reagent derived from ring-opening metathesis polymerization (ROMP) is reported as an effective coupling reagent, scavenger of nucleophilic species, and activator of DMSO for the classic Swern oxidations. Two variants of this reagent (2G)ODCT 4 and (1G)ODCT 16, possessing theoretical loads of 5.3 and 7.3 mmol/g, respectively, have been synthesized. Preparation was accomplished via simple synthetic protocols affording free flowing powders, amenable for large-scale production. Removal of the spent oligomeric reagent was achieved via either precipitation of the spent reagent or simple filtration utilizing a silica SPE, followed by solvent removal, to deliver products in excellent yield and purity. In addition, the corresponding norbornenyl monomer 3 was successfully demonstrated in a couple-ROMP-filter protocol utilizing in situ polymerization, achieving comparable results versus the corresponding oligomeric variant.

Oligomeric Benzylsulfonium Salts: Facile Benzylation via High-Load ROMP Reagents

The development of high-load, oligomeric benzylsulfonium salts, generated via ring-opening metathesis polymerization, and their utility in facile benzylations of various nucleophiles is reported. These oligomeric sulfonium salts exist as free-flowing powders and are stable at room temperature. After the benzylation event, purification is attained via simple dry load/filtration, followed by solvent removal to deliver products in excellent yield and purity.

Pyrrolizidine Esters and Amides as 5-HT4 Receptor Agonists and Antagonists

A series of pyrrolizidine esters, amides, and ureas was prepared and tested for 5-HT(4) and 5-HT(3) receptor binding, 5-HT(4) receptor agonism in the rat tunica muscularis mucosae (TMM) assay, and for 5-HT(3) receptor-mediated functional antagonism in the Bezold-Jarisch reflex assay. Several pyrrolizidine derivatives were identified with high affinity for the 5-HT(4) receptor, including benzamide 12a (SC-53116), a potent and selective 5-HT(4) partial agonist that exhibits efficacy in promoting antral contractions and activity in promoting gastric emptying in canine models. Also discovered were 5-HT(4) receptor antagonists, including imidazopyridine amide 12h (SC-53606), which is a potent and selective 5-HT(4) receptor antagonist with a pA(2) value of 8.13 in the rat TMM assay. N-Methyl indole ester 13d was identified as a potent 5-HT(4) antagonist with a pA(2) value of 8.93. High selectivity was observed for these pyrrolizidine derivatives versus other monoamine receptors, including 5-HT(1), 5-HT(2), D(1), D(2), alpha(1), alpha(2), and beta receptors.

Multipolymer solution-phase reactions: application to the Mitsunobu reaction

The realization of the first polymer-on-polymer Mitsunobu reaction, in which a polymeric phosphine is used simultaneously with a polymeric azodicarboxylate, is reported. This strategy employs the use of soluble oligomers generated from ring-opening methathesis polymerization. 31P NMR analysis revealed that the two polymers were interacting to generate the Mitsunobu products. Application to several substrates, as well as comparison experiments with other polymeric reagents, is described.

High-Load, Soluble Oligomeric Carbodiimide: Synthesis and Application in Coupling Reactions

A facile preparation of a high-load, soluble oligomeric alkyl cyclohexylcarbodiimide (OACC) reagent via ROM polymerization from commercially available starting materials is described. This reagent is exploited as a coupling reagent for esterification, amidation, and dehydration of carboxylic acids (aliphatic and aromatic) with an assortment of alcohols (aliphatic primary, secondary, and benzylic), thiols, phenols, and amines (aliphatic primary, secondary, benzylic, and aromatic/anilines), respectively. Following the coupling event, precipitation with an appropriate solvent (Et(2)O, MeOH, or EtOAc), followed by filtration through a SPE provides the products in good to excellent yield and purity.

Azaadamantane benzamide 5-HT4 agonists: gastrointestinal prokinetic SC-54750

Azaadamantanone 1 was converted to a series of aminoazaadamantane benzamides 9a-d, which were profiled for serotonin receptor activity. Aminomethylazaadamantane SC-54750 is a potent 5-HT(4) agonist and 5-HT(3) antagonist with in vivo efficacy in gastroparesis models and also inhibits cisplatin-induced emesis.

Development of High-Load, Soluble Oligomeric Sulfonate Esters via ROM Polymerization: Application to the Benzylation of Amines

The development of high-load, soluble oligomeric sulfonate esters, generated via ROM polymerization, and their utility in the facile benzylation of an array of amines is reported. These polymeric sulfonate esters exist as free-flowing powders, are stable at refrigerated temperatures, and are readily dissolved in CH(2)Cl(2). Following the benzylation event, purification is attained via simple filtration, followed by solvent removal to deliver the desired benzylated product in good to excellent yield and high purity. [structure: see text]

Bridgehead-methyl analog of SC-53116 as a 5-HT4 agonist

Pyrrolizidine benzamide (+/-)-2, the bridgehead-methyl analog of SC-53116, was prepared and evaluated for 5-HT(4) agonism activity in the rat tunica muscularis (TMM) mucosae assay. Compound (+/-)-2 has an EC(50) of 449 nM in the TMM assay, as compared to 23 nM for SC-53116, and 66 nM for the racemate of SC-53116.