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 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 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.

The 15-Amino Acid Repeat Region of Adenomatous Polyposis Coli Is Intrinsically Disordered and Retains Conformational Flexibility upon Binding β-Catenin

The tumor suppressor Adenomatous polyposis coli (APC) is a large, multidomain protein with many identified cellular functions. The best characterized role of APC is to scaffold a protein complex that negatively regulates Wnt signaling via β-catenin destruction. This destruction is mediated by β-catenin binding to centrally located 15- and 20-amino acid repeat regions of APC. More than 80% of cancers of the colon and rectum present with an APC mutation. Most carcinomas with mutant APC express a truncated APC protein that retains the ∼200-amino acid long' 15-amino acid repeat region'. This study demonstrates that the 15-amino acid repeat region of APC is intrinsically disordered. We investigated the backbone dynamics in the presence of β-catenin and predicted residues that may contribute to transient secondary features. This study reveals that the 15-amino acid region of APC retains flexibility upon binding β-catenin and that APC does not have a single, observable "highest-affinity" binding site for β-catenin. This flexibility potentially allows β-catenin to be more readily captured by APC and then remain accessible to other elements of the destruction complex for subsequent processing.

Oncogenic Serine 45-Deleted β-Catenin Remains Susceptible to Wnt Stimulation and APC Regulation in Human Colonocytes

The Wnt/β-catenin signaling pathway is deregulated in nearly all colorectal cancers (CRCs), predominantly through mutation of the tumor suppressor Adenomatous Polyposis Coli (APC). APC mutation is thought to allow a “just-right” amount of Wnt pathway activation by fine-tuning β-catenin levels. While at a much lower frequency, mutations that result in a β-catenin that is compromised for degradation occur in a subset of human CRCs. Here, we investigate whether one such “stabilized” β-catenin responds to regulatory stimuli, thus allowing β-catenin levels conducive for tumor formation. We utilize cells harboring a single mutant allele encoding Ser45-deleted β-catenin (β-catΔS45) to test the effects of Wnt3a treatment or APC-depletion on β-catΔS45 regulation and activity. We find that APC and β-catΔS45 retain interaction with Wnt receptors. Unexpectedly, β-catΔS45 accumulates and activates TOPflash reporter upon Wnt treatment or APC-depletion, but only accumulates in the nucleus upon APC loss. Finally, we find that β-catenin phosphorylation at GSK-3β sites and proteasomal degradation continue to occur in the absence of Ser45. Our results expand the current understanding of Wnt/β-catenin signaling and provide an example of a β-catenin mutation that maintains some ability to respond to Wnt, a possible key to establishing β-catenin activity that is “just-right” for tumorigenesis.