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DNA methylation, a key epigenetic driver of transcriptional silencing, is universally dysregulated in cancer. Reversal of DNA methylation by hypomethylating agents, such as the cytidine analogs decitabine or azacytidine, has demonstrated clinical benefit in hematologic malignancies. These nucleoside analogs are incorporated into replicating DNA where they inhibit DNA cytosine methyltransferases DNMT1, DNMT3A and DNMT3B through irreversible covalent interactions. These agents induce notable toxicity to normal blood cells thus limiting their clinical doses. Herein we report the discovery of GSK3685032, a potent first-in-class DNMT1-selective inhibitor that was shown via crystallographic studies to compete with the active-site loop of DNMT1 for penetration into hemi-methylated DNA between two CpG base pairs. GSK3685032 induces robust loss of DNA methylation, transcriptional activation and cancer cell growth inhibition in vitro. Due to improved in vivo tolerability compared with decitabine, GSK3685032 yields superior tumor regression and survival mouse models of acute myeloid leukemia.

BackgroundAlthough immunotherapy produced dramatic clinical responses in a certain population of cancer patients, tumor cells can employ a variety of immunosuppressive measures to limit the immunotherapeutic efficacy. This highlights a great need to develop novel strategies to expand the clinical benefits of immunotherapy to a broader population of cancer patients. PRMTs have been described as vital regulators of immune responsive pathways in several cell types, but the immunoregulatory role of Type I PRMTs in the tumor microenvironment remains poorly understood.MethodsIn this study, we analyzed the correlation between Type I PRMT expression levels with the clinical outcome or immune signature. Gene expression changes were evaluated in a panel of immunogenic and non-immunogenic cancer cell lines with Type I PRMT inhibitor treatment. The antitumor and immunological effects of Type I PRMT inhibitor were evaluated in combination with checkpoint blockade in a panel of syngeneic tumor models.ResultsUsing TCGA dataset analysis, increased mRNA expression levels of several Type I PRMTs were associated with poor clinical response and decreased immune infiltration in melanoma patients. Particularly, tumors with high expression of PRMT1, the major Type I PRMTs, displayed significantly reduced relapse-free survival (HR=1.891, p=0.038), and were associated with lower cytolytic score (logFC=-0.875, p=1.49e-08) and lower lymphocyte infiltration score (logFC=-0.783, p=0.00077). RNA-seq results showed that interferon signaling was significantly altered after Type I PRMT inhibitor treatment in 10 of 15 cell lines analyzed, with most related genes showing increased expression. In addition, VEGFA was downregulated by 25% or more in 7/8 human and 3/5 mouse cancer cell lines, and a moderate decrease in chromatin accessibility at the Vegfa promoter was observed in ATAC-seq data. Furthermore, Type I PRMT inhibitor combined with anti-PD1 treatment significantly extended the survival of tumor-bearing mice and delayed tumor growth in a panel of immunocompetent mouse models. Mechanistically, Type I PRMT inhibitor significantly increased the apoptotic sensitivity of tumor cells to autologous tumor-reactive T cells in vitro and the infiltration of total T cells (CD3+) in 3 of 4 tested tumor models and cytotoxic T cells (CD8+) in two tested tumor models in vivo.ConclusionsTaken together, these data indicated that Type I PRMT inhibition exhibits immunomodulatory properties and synergizes with immune checkpoint blockade to induce durable antitumor responses in a T cell dependent manner. This study provides a rationale to combine Type I PRMT inhibitor with immune checkpoint blockade to maximize clinical benefits in cancer patients.AcknowledgementsThe authors would like to thank past and present members of the MDACC TIL lab for tumor/TIL processing and banking.

Aberrant DNA hypermethylation within promoter regions and subsequent gene silencing are near universal hallmarks of human cancer. Reversal of DNA methylation by a hypomethylating agent, such as decitabine (Dacogen) or azacytidine (Vidaza), has shown clinical benefit for the treatment of heme malignancies. However, these agents have several limitations that preclude their full potential from being realized such as the requirement for IV administration, poor PK properties and a mechanism that requires incorporation into replicating DNA. This indirect, irreversible inhibition of the DNA methyltransferase (DNMT) family (DNMT1, 3a and 3b) and subsequent DNA damage induces significant dose-limiting toxicity thus preventing sufficient target engagement required for maximal demethylation. A drug discovery effort focused on DNMT1, the key family member responsible for maintaining the DNA methylation pattern, was initiated based on the compelling nature of the target coupled with the need for improved agents. A high-throughput screen identified a single dicyanopyridine (DCP) series of reversible, non-DNA incorporating, highly selective inhibitors for DNMT1 over DNMT3a or DNMT3b. Ensuing structure-activity relationship (SAR) optimization of the series led to the discovery of potent tool compounds that in cancer cells induced robust decreases in global DNA methylation, transcriptional activation of many silenced genes, and inhibition of cancer cell growth. In contrast to decitabine where most cells showed a cytotoxic response, our DNMT1 tool inhibitors primarily elicited a cytostatic response. Furthermore, studies in a mouse tumor model revealed decreased DNA methylation and a dose-dependent (1-45 mg/kg, BID) decrease in tumor growth with regression at the highest doses. In summary, a series of potent, selective DNMT1 inhibitors were discovered and refined delivering tool compounds capable of eliciting changes in DNA methylation, transcriptional activation, and tumor regression at well-tolerated doses. Thus demonstrating that selective, non-covalent inhibitors of DNMT1 may provide benefit over traditional DNA incorporating hypomethylating agents. Citation Format: Melissa B. Pappalardi, Mark Cockerill, Jessica L. Handler, Alexandra Stowell, Kathryn Keenan, Christian S. Sherk, Elisabeth A. Minthorn, Charles F. McHugh, Charlotte Burt, Kristen Wong, David T. Fosbenner, Mehul Patel, Jacques Briand, Helai Mohammad, Lourdes Rueda, Andrew Benowitz, Rab Prinjha, Dirk Heerding, Ryan G. Kruger, Ali Raoof, Allan Jordan, Bryan W. King, Michael T. McCabe. Discovery of selective, noncovalent small molecule inhibitors of DNMT1 as an alternative to traditional DNA hypomethylating agents [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 2994.

Elevated expression of the c-MYC oncogene (either due to gene amplification, translocation, abnormality in upstream signaling pathways and/or protein stabilization) is one of the most common abnormalities in human cancers. Efforts to identify direct pharmacological inhibitors of c-MYC function have not yet yielded drug-like molecules. Therefore, we sought to pursue alternative screening strategies for this classically “undruggable” transcription factor. We developed a novel antibody-based high-throughput HTRF screening assay that specifically detects endogenous c-MYC protein levels in a MYC amplified cancer cell line. Taking advantage of the short half-life of c-MYC, both at the protein and mRNA level, we conducted a cell-based screen of the GSK screening collection to identify compounds that can rapidly decrease c-MYC protein levels. Elimination of false positive hits using stringent triage assays successfully identified two valid hit series exemplified by GSK970 and GSK417. Molecular mode of action studies revealed these molecules inhibit MYC transcription by binding to the minor groove of DNA with AT sequence specificity. Unfortunately, this mechanism of c-MYC inhibition demonstrated poor in vivo translatability as tissue DNA acts as a molecular sink, effectively sequestering compound, and limiting its pharmacodnyamic response. Citation Format: Biju Mangatt, Anthony D. Pietra, Anna Waszkiewicz, Jon-Paul Jaworski, Sonja Ghidelli-Disse, Thomas J. Berrodin, Christian S. Sherk, Derrick W. Meinhold, Anna Rutkowska-Klute, Shanker K. Sundaram, Gopinath Ganji, Wendy S. Halsey, George P. Livi, William Li, James Mack, Stuart P. Romeril, Elisabeth A. Minthorn, Rakesh Kumar, Gerard C. Drewes, Dirk A. Heerding, Lorena A. Kallal, Carolyn A. Buser, Jesus R. Medina. Discovery of small-molecule compounds targeting c-MYC using a novel cell-based screen [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 2919.

Fibroblast growth factor (FGF) ligand-dependent signaling has a fundamental role in cancer development and tumor maintenance. GSK3052230 (also known as FP-1039) is a soluble decoy receptor that sequesters FGFs and inhibits FGFR signaling. Herein, the efficacy of this molecule was tested in models of mesothelioma, a tumor type shown to express high levels of FGF2 and FGFR1. GSK3052230 demonstrated antiproliferative activity across a panel of mesothelioma cell lines and inhibited growth of tumor xenografts in mice. High expression of FGF2 and FGFR1 correlated well with response to FGF pathway inhibition. GSK3052230 inhibited MAPK signaling as evidenced by decreased phospho-ERK and phospho-S6 levels in vitro and in vivo. Additionally, dose-dependent and statistically-significant reductions in tumor vessel density were observed in GSK3052230-treated tumors compared to vehicle-treated tumors. These data support the role of GSK3052230 in effectively targeting FGF-FGFR autocrine signaling in mesothelioma, demonstrate its impact on tumor growth and angiogenesis, and provide a rationale for the current clinical evaluation of this molecule in mesothelioma patients.

A novel thiazolopyrimidinone series of PI3K-beta selective inhibitors has been identified. This chemotype has provided an excellent tool compound, 18, that showed potent growth inhibition in the PTEN-deficient breast cancer cell line MDA-MB-468 under anchorage-independent conditions, and it also demonstrated pharmacodynamic effects and efficacy in a PTEN-deficient prostate cancer PC-3 xenograft mouse model.

Fibroblast growth factor (FGF) ligand-dependent signaling plays an important role in cancer development and tumor maintenance through autocrine production of FGFs directly from cancer cells and/or through paracrine production of FGFs from the local stroma. FGF-FGFR autocrine feedback loops have been characterized in several tumor types and may also play a role in drug resistance upon exposure to chemotherapy or targeted agents. FP-1039/GSK3052230 is a ligand trap that sequesters multiple FGFs and inhibits FGF receptor signaling. We previously demonstrated that increased FGF2 mRNA levels correlated with response to GSK3052230. To further extend this hypothesis, we investigated the preclinical efficacy of this drug in models of mesothelioma, a tumor type shown to express high levels of FGF2 mRNA in cell lines and in primary tumor specimens. GSK3052230 inhibited MAPK signaling as evidenced by decreased phospho-ERK levels in both NCI-H226 and MSTO-211H cells. When both cell lines were grown as tumor xenografts in mice, GSK3052230 inhibited tumor growth in a dose-dependent manner (NCI-H226: 16 - 78% TGI; MSTO-211H: 20 - 50% TGI). However, in contrast to what was observed in cultured cells, GSK3052230 had minimal effects on phospho-ERK levels in NCI-H226 tumors. Similarly, two genes downstream of ERK known to be regulated by FGF signaling, DUSP6 and ETV4, displayed modestly reduced mRNA levels upon GSK3052230 treatment. These data demonstrate the limitation of FGF pathway downstream signaling as a pharmacodynamic (PD) readout for this drug in this study despite observing significant tumor growth inhibition. Because FGFs also play a key role in angiogenesis, we explored the effects of GSK3052230 on tumor vessel formation in NCI-H226 xenografts as a potential approach to measure PD. Dose-dependent and statistically-significant reductions in tumor vessel density were observed in GSK3052230-treated tumors compared to vehicle-treated tumors using MECA-32 endothelial cell immunohistochemical staining. These data support the clinical evaluation of this drug in mesothelioma patients. Citation Format: M. Phillip De Young, Christian Sherk, Maureen Bleam, Mary Barnette, Gopi Ganji, Bao Hoang, James Tunstead, David Bellovin, Gerrit Los, Elisabeth Minthorn, Rakesh Kumar. Preclinical efficacy of targeting FGF autocrine signaling in mesothelioma with the FGF ligand trap, FP-1039/GSK3052230. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-236. doi:10.1158/1538-7445.AM2014-LB-236

Many cancer cells generate energy by rapidly converting glucose to lactate in the cytosol, a process termed aerobic glycolysis. This metabolic phenotype is recognized as one of the hallmarks of cancer and is enabled by lactate dehydrogenase (LDH), which catalyzes pyruvate to lactate inter-conversion. We find that hepatocellular carcinoma cells express micromolar quantities of LDH5 and that LDH5 protein down-regulation takes about 5 days allowing time for the cells to adapt their metabolism. Since metabolic processes happen in minutes, addressing consequences of LDH5 inhibition by protein down-regulation is inadequate. We screened the GSK compound library and identified a series of quinoline acids as NADH-competitive LDH5 inhibitors. Subsequent lead optimization yielded molecules with LDH5 inhibitory potencies as low as 2-3 nM and selectivity over LDH1 on the order of 10-100-fold. These molecules were cell-permeable and did not have any appreciable activity against a panel of approximately fifty common enzymes, receptors and ion channels, making them the most potent and selective LDH5 inhibitors identified to date. Using these tool inhibitors, we find that rapid chemical inhibition of LDH5 in Snu398 hepatocellular carcinoma cells results in profound inhibition of lactate production and increase in pyruvate as measured by mass spectrometric analysis. Real-time analysis by NMR spectroscopy of live Snu398 cells fed with 13C-labeled glucose demonstrated that chemical LDH5 inhibition led to a rapid decrease in glucose uptake and concomitant slow-down of lactate production. Comprehensive analysis of more than 500 metabolites upon LDH5 inhibition in Snu398 cells revealed that the cytosolic glycolysis pathway was significantly impeded with some up-stream intermediates increasing as much as 40-fold. As the cell lost its ability for cytosolic glucose processing, the TCA cycle activity increased indicating that pyruvate entered the mitochondria and restored their activity resulting in increased oxygen consumption upon LDH5 inhibition. Several pathways that rely on glycolytic and TCA intermediates were also upregulated, including fatty acid metabolism and pentose phosphate pathway. LDH5 inhibition also strongly potentiated PKM2 activity. These profound metabolic alterations greatly impaired cell survival and induced cell death in Snu398 cells. In summary, we have shown that rapid chemical inhibition of LDH5 leads to profound metabolic alterations and impairs cell survival in hepatocellular carcinoma cells making it a compelling strategy for treating solid tumors relying on aerobic glycolysis. Citation Format: Julia Billiard, Roland Annan, Jennifer Ariazi, Jacques Briand, Kristin Brown, Nino Campobasso, Subhas Chakravorty, Deping Chai, Mariela Colón, Elizabeth Davenport, Christopher Dodson, Nathan Gaul, Seth Gilbert, Anthony Jurewicz, Hong Lu, Dean McNulty, Jeanelle McSurdy-Freed, Lisa Miller, Kelvin Nurse, Paru Rao Nuthulaganti, Chad Quinn, Jessica Schneck, Gilbert Scott, Tony Shaw, Christian Sherk, Angela Smallwood, Sharon Sweitzer, James Villa, Gregory Waitt, Richard Wooster, Kevin Duffy. Rapid LDH5 inhibition reverses malignant metabolic phenotype and impairs survival of hepatocellular carcinoma cells . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5418. doi:10.1158/1538-7445.AM2013-5418