USP7 inhibitors suppress tumour neoangiogenesis and promote synergy with immune checkpoint inhibitors by downregulating fibroblast VEGF

BACKGROUND

Understanding how to modulate the microenvironment of tumors that are resistant to immune checkpoint inhibitors represents a major challenge in oncology.Here we investigate the ability of USP7 inhibitors to reprogram the tumor microenvironment (TME) by inhibiting secretion of vascular endothelial growth factor (VEGF) from fibroblasts.

METHODS

To understand the role played by USP7 in the TME, we systematically evaluated the effects of potent, selective USP7 inhibitors on co-cultures comprising components of the TME, using human primary cells. We also evaluated the effects of USP7 inhibition on tumor growth inhibition in syngeneic models when dosed in combination with immune checkpoint inhibitors (ICIs).

RESULTS

Abrogation of VEGF secretion from fibroblasts in response to USP7 inhibition resulted in inhibition of tumor neoangiogenesis and increased tumor recruitment of CD8-positive T-lymphocytes, leading to significantly improved sensitivity to immune checkpoint inhibitors. In syngeneic models, treatment with USP7 inhibitors led to striking tumor responses resulting in significantly improved survival.

CONCLUSIONS

USP7-mediated reprograming of the TME is not linked to its previously characterized role in modulating MDM2 but does require p53 and UHRF1 in addition to the well-characterized VEGF transcription factor, HIF-1α. This represents a function of USP7 that is unique to fibroblasts, and which is not observed in cancer cells or other components of the TME. Given the potential for USP7 inhibitors to transform "immune desert" tumors into "immune responsive" tumors, this paves the way for a novel therapeutic strategy combining USP7 inhibitors with immune checkpoint inhibitors (ICIs).

Abstract 3449: Development of MRT-2359, an orally bioavailable GSPT1 molecular glue degrader, for the treatment of lung cancers with MYC-induced translational addiction

MYC transcription factors are well-established drivers of human cancers but despite being amongst the most frequently altered oncogenes, no approved therapy targeting MYC-driven tumors has been developed to date. MYC-driven cancers are known to be addicted to protein translation. This addiction creates a dependency on critical components of the translational machinery providing in turn a unique opportunity for therapeutic intervention. We hypothesized that targeting the translation termination factor GSPT1, a key regulator of protein synthesis, would constitute a vulnerability for MYC-driven tumors. Herein we further describe MRT-2359 a potent, selective and orally bioavailable degrader of GSPT1. MRT-2359 was rationally designed using our QuEENTM discovery engine and optimized to achieve a profound and preferential antiproliferative activity in MYC-driven cell lines, such as high N- and L-MYC mRNA expressing non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) lines. In line with expectations, MRT-2359 activity is dependent on both CRBN and the GSPT1 G-loop degron. We further demonstrate using an inducible system that the sole expression of either N- or L-MYC is sufficient to sensitize initially resistant NSCLC cells to MRT-2359. These studies therefore establish a causal link between N- and L-MYC expression and sensitivity to MRT-2359. Unlike MRT-2359, agents targeting the protein translation initiation machinery or repressing MYC transcription (CDK9 inhibitor) failed to show such differential activity. Mechanistically, RiboSeq and polysome profiling revealed that treatment with MRT-2359 in the N- or L-MYC high cell lines induces ribosome stalling at the stop codon, increased monosomes and decreased polysomes. These changes are indicative of translational repression and were confirmed using puromycilation assays. Proteomics and RNAseq studies finally demonstrated a significant reduction in the total levels of N- or L-MYC leading in turn to the downmodulation of MYC target genes. Despite robust degradation of GSPT1, no marked effect was observed in these assays in low N- or L-MYC lines, confirming the selective activity of MRT-2359 in MYC-driven lung cancers. Last, the anti-tumor activity of MRT-2359 was assessed in >80 lung patient-derived xenografts (PDXs). MRT-2359 demonstrated preferential activity in N- and L-MYC high NSCLC and SCLC PDXs, including numerous instances of tumor regressions, when dosed orally daily or intermittently. Similar levels of anti-tumor activity were also observed in neuroendocrine lung cancer and lymphoma PDXs. Together these results warrant further investigations in the clinic. Oral MRT-2359 is currently in a Phase 1/2 clinical trial in selected cancer patients with MYC-driven NSCLC, SCLC, high grade neuroendocrine cancers and diffuse large B-cell lymphoma (NCT05546268).

Citation Format: Gerald Gavory, Mahmoud Ghandi, Anne-Cecile d’Alessandro, Debora Bonenfant, Maciej Cabanski, Lisa Cantagallo, Agustin Chicas, Qian Chen, Anna Diesslin, Christopher King, Vittoria Massafra, Rajiv Narayan, Arnaud Osmont, Dave Peck, Carolina Perdomo Ortiz, Martin Schillo, Ambika Singh, Ralph Tiedt, Simone Tortoioli, Silvia Buonamici, Filip Janku, Owen Wallace, Bernhard Fasching. Development of MRT-2359, an orally bioavailable GSPT1 molecular glue degrader, for the treatment of lung cancers with MYC-induced translational addiction [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 3449.

Identification and development of a subtype-selective allosteric AKT inhibitor suitable for clinical development

The serine/threonine protein kinase AKT plays a pivotal role within the PI3K pathway in regulating cellular proliferation and apoptotic cellular functions, and AKT hyper-activation via gene amplification and/or mutation has been implicated in multiple human malignancies. There are 3 AKT isoenzymes (AKT1-3) which mediate critical, non-redundant functions. We present the discovery and development of ALM301, a novel, allosteric, sub-type selective inhibitor of AKT1/2. ALM301 binds in an allosteric pocket created by the combined movement of the PH domain and the catalytic domain, resulting in a DFG out conformation. ALM301 was shown to be highly selective against a panel of over 450 kinases and potently inhibited cellular proliferation. These effects were particularly pronounced in MCF-7 cells containing a PI3KCA mutation. Subsequent cellular downstream pathway analysis in this sensitive cell line revealed potent inhibition of pAKT signalling up to 48 h post dosing. ALM301 treatment was well tolerated in an MCF-7 xenograft model and led to a dose-dependent reduction in tumour growth. Enhanced efficacy was observed in combination with tamoxifen. In summary, ALM301 is a highly specific AKT 1/2 inhibitor with an excellent pharmacological profile suitable for further clinical development.

Abstract 3929: Identification of MRT-2359 a potent, selective and orally bioavailable GSPT1-directed molecular glue degrader (MGD) for the treatment of cancers with Myc-induced translational addiction

Myc transcription factors are well-established drivers of human cancers. However, despite being amongst the most frequently mutated, translocated and overexpressed oncogenes, no therapy targeting the Myc family members directly has been developed to date. To sustain uncontrolled cell proliferation and tumor growth, Myc-driven cancers are known to be addicted to protein translation. This addiction creates a dependency on critical components of the translational machinery providing in turn a unique opportunity for therapeutic intervention. We hypothesized that targeting the translational termination factor GSPT1, a key regulator of protein synthesis, would constitute a vulnerability for Myc-driven tumors. GSPT1 contains a well-defined degron allowing for the recruitment of the E3 ligase cereblon (CRBN) and subsequent proteasomal degradation in the presence of molecular glue degraders. Herein we describe a novel orally bioavailable GSPT1-directed small molecule degrader MRT-2359, which has been rationally designed and optimized to selectively induce apoptosis in translationally addicted cells. MRT-2359 promotes complex formation between CRBN and GSPT1 and potently induces GSPT1 degradation in a CRBN- and degron-dependent manner. The high selectivity of MRT-2359 was subsequently demonstrated by the lack of activity in cells expressing a non-degradable GSPT1 mutant. Although MRT-2359 degrades GSPT1 in all the cell lines tested, profiling in a large panel of cancer lines revealed profound and preferential antiproliferative activity in Myc-driven cell lines, such as high N-Myc expressing non-small cell lung cancer (NSCLC) lines and high L-Myc expressing small cell lung cancer (SCLC) lines. In the Myc-driven cells, degradation of GSPT1 led to translational repression as manifested by a global shift from polysomes to monosomes resulting in the reduction of a subset of proteins as assessed by quantitative proteomics. In particular, N- or L-Myc protein levels decreased and as a consequence the known Myc target genes were downregulated at the mRNA level. Despite the robust degradation of GSPT1, no marked effect was observed in low N-Myc lines, confirming the selective activity of our GSPT1 degrader in Myc-driven lung cancers. Finally, oral administration of MRT-2359 in high N-Myc NSCLC xenografts and PDXs led to complete intratumoral GSPT1 degradation and concomitant decrease in N-Myc protein levels, resulting in tumor regression. In contrast, MRT-2359 had limited or no activity in low N-Myc NSCLC models, further corroborating the selective vulnerability of Myc-driven tumors to GSPT1 degradation. Together these data support the therapeutic potential of GSPT1-directed MGDs in Myc-driven solid tumors addicted to the protein translation machinery and warrant rapid evaluation towards the clinic.

Citation Format: Gerald Gavory, Mahmoud Ghandi, Anne-Cecile d’Alessandro, Debora Bonenfant, Agustin Chicas, Frederic Delobel, Brad Demarco, Alexander Flohr, Christopher King, Anne-Laure Laine, Vittoria Massafra, Rajiv Narayan, Arnaud Osmont, Giorgio Ottaviani, Dave Peck, Sarah Pessa, Nooreen Rubin, Thomas Ryckmans, Martin Schillo, Ambika Singh, Simone Tortoioli, Dominico Vigil, Vladislav Zarayskiy, John Castle, Filip Janku, Owen Wallace, Silvia Buonamici, Bernhard Fasching. Identification of MRT-2359 a potent, selective and orally bioavailable GSPT1-directed molecular glue degrader (MGD) for the treatment of cancers with Myc-induced translational addiction [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 3929.

Abstract LBA004: Identification of GSPT1-directed molecular glue degrader (MGD) for the treatment of Myc-driven breast cancer

The Myc family of transcription factors is a well-established driver of human cancers. However, despite being amongst the most frequently mutated, translocated and overexpressed oncogenes, no therapy directly targeting the Myc family members has been developed to date. Abnormal activation of Myc results in uncontrolled cell growth that is associated with high translational output and ramp up of the protein translational machinery. This creates a dependency to protein translation and in turn represents a potential therapeutic vulnerability for Myc-driven tumors. Based on these considerations, we hypothesized that targeting the translational termination factor GSPT1, a key player of protein synthesis, may constitute a vulnerability for Myc-driven tumors. Using our proprietary Quantitative and Engineered Elimination of Neosubstrates (QuEENTM) platform we characterized and explored the known G-loop degron in GSPT1 that renders it amenable to cereblon-induced degradation by molecular glue degraders (MGDs). We rationally designed and subsequently screened a proprietary library of cereblon-binding small molecules, including GSPT1-directed MGDs, in human mammary epithelial cells (HMECs) expressing doxycycline-inducible c-Myc. Doxycycline treatment led to sustained c-Myc expression and as a consequence to the induction of key biomarkers of enhanced protein translation, such as phospho 4EBP1 (p4EBP1). We identified MRT-048 as a potent and highly selective GSPT1 degrader and demonstrated its ability to induce cell death in Myc-driven HMEC cells whilst sparing control cells (EC50 0.64 μM vs 30 μM respectively). This confirmed the selective vulnerability of Myc-driven cell growth to GSPT1 degradation. In follow-up studies, we confirmed the correlation between p4EBP1 as biomarker of Myc-activation and sensitivity to MRT-048 in a large panel of breast cancer cell lines. Moreover, MRT-048 treatment of animals xenografted with breast cancer cells induced tumor regression and was associated with complete GSPT1 degradation. Mechanistically, we observed that GSPT1 degradation induced by MRT-048 led to inhibition of genes regulated by Myc and ribosomal stalling at stop codons of several mRNAs. Additionally, polysome profiling of cancer cells treated with MRT-048 was associated with a global reduction of the intensities of the polysome peaks and concomitant increase in the monosome peaks as previously observed in GSPT1 knockdown experiments, suggesting that GSPT1 degradation by our MGD molecules affects both the termination and initiation stages of protein translation. We believe these data support the therapeutic potential of GSPT1-directed MGDs in Myc-driven tumors dependent on protein translation machinery.

Citation Format: Gerald Gavory, Bernhard Fasching, Debora Bonenfant, Amine Sadok, Ambika Singh, Martin Schillo, Vittoria Massafra, Anne-Cecile d’Alessandro, John Castle, Mahmoud Ghandi, Agustin Chicas, Frederic Delobel, Alexander Flohr, Giorgio Ottaviani, Thomas Ryckmans, Anne-Laure Laine, Oliv Eidam, Hannah Wang, Ilona Bernett, Laura Chan, Chiara Gorrini, Theo Roumiliotis, Jyoti Choudhary, Yann-Vai LeBihan, Marc Cabry, Mark Stubbs, Rosemary Burke, Rob Van Montfort, John Caldwell, Rajesh Chopra, Ian Collins, Silvia Buonamici. Identification of GSPT1-directed molecular glue degrader (MGD) for the treatment of Myc-driven breast cancer [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 LBA004.

Abstract LB-087: Discovery and development of first-in-class orally bioavailable USP19 inhibitors

Over the past decade, protein ubiquitination has emerged as an important post-translational modification with regulatory functions in all important cellular processes. Deubiquitinating enzymes (DUBs) including ubiquitin specific proteases (USPs) catalyse the de-ubiquitination of protein substrates, hence regulating their levels and/or function. As a result of their increasing implications in the aetiology of numerous pathological conditions including cancer, neurodegeneration and metabolic disorders, DUBs represent an attractive and promising target class for the development of innovative medicines with high therapeutic impact. However, despite 15 years of research DUBs have proved largely refractory to drug discovery efforts.

As a result of genetic and other validation studies, USP19 has recently emerged as a potentially important target in muscular atrophy associated with various conditions including cancer, as well as in other disorders involving aberrant protein quality control. Herein, we describe the application of our Ubi-Plex™ drug discovery platform to the identification and optimisation of first in class USP19 inhibitors. Several series of novel, highly potent (e.g. IC50 < 5.0 nM) and reversible USP19 inhibitors have been identified. Further profiling has demonstrated excellent selectivity against a large panel of DUBs and other non-related enzymes (e.g. kinases, proteases). These inhibitors are cell-permeable and exhibit potent target engagement in both cancer and muscle cells with EC50 values < 30 nM. We will describe the development of lead molecules with drug-like properties which have allowed us to establish pharmacological target validation by demonstrating efficacy in a muscle wasting model in vivo. Recent developments in the programme leading to orally available USP19 inhibitors will also be presented. This work further exemplifies the tractability of the DUB target family and reports the discovery and detailed profiling of first-in-class inhibitors of USP19. These findings support the rationale to target USP19 for debilitating muscle wasting disorders associated with various conditions such as cancer, as well as for potentially other therapeutic indications, particularly those associated with aberrant protein quality control.

Citation Format: Xavier Jacq, Gerald Gavory, Colin O'Dowd, Aaron Cranston, Oliver Baker, Christina Bell, Stephanie Burton, Eamon Cassidy, Joana Costa, Ashling Henderson, Matthew Helm, Peter Hewitt, Caroline Hughes, Mary McFarland, Hugues Miel, Lauren Proctor, Shane Roundtree, Rachel Church, Ewelina Rozycka, Mark Wappett, Steven Whitehead, Tim Harrison, Nathalie Bedard, Simon S. Wing. Discovery and development of first-in-class orally bioavailable USP19 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-087.

Abstract LB-049: Targeting the ubiquitin-proteasome system by small molecule inhibition of the DUBome

The current interest in protein homeostasis as a therapeutic strategy has highlighted the importance of protein ubiquitination as a post-translational modification. Protein degradation has been enabled by several approaches (e.g. small molecule degraders, molecular glues, and PROTACsTM). Deubiquitinating enzymes (DUBs) are proteases that catalyse the de-ubiquitination of protein substrates and as such offer an alternative way to regulate protein homeostasis. Furthermore, since ubiquitination also controls a plethora of regulatory functions beyond direct degradation, inhibition of DUBs provides additional opportunities to manipulate critical cellular processes. As a result of this dual role in protein degradation and signalling, as well as their increasing linkage to the etiology of numerous pathological conditions including cancer and neurodegeneration, DUBs have emerged as an attractive target class for the development of first-in-class medicines with high therapeutic impact. However until recently, DUBs have proven largely refractory to drug discovery efforts despite significant industry efforts. We have developed a purpose-built drug discovery platform (UbiPlex™) for the identification and development of DUB inhibitors. Herein, we will highlight significant recent developments to this platform including the addition of multiple DUB crystal structures (including fragments and small molecule co-crystals), biophysics, chemo/bio-informatics capabilities and focussed screening libraries. These developments have allowed the identification of novel, highly potent (e.g. IC50 < 100 nM), reversible inhibitors with drug like properties against multiple therapeutically relevant DUB targets. Selectivity profiles of representative inhibitors against panels of DUBs and other non-related enzymes (e.g. kinases, proteases) will be described, demonstrating that excellent selectivity is achievable. Finally, we will describe our progress towards the development of lead molecules with drug-like properties with the aim of rapidly establishing proof-of-concept studies in vivo for previously unexplored DUB targets. This work exemplifies the broad tractability and druggability of the DUBome and provides an alternative strategy for manipulation of the UPS. Furthermore, these potent, selective, cell penetrant molecules represent important chemical probes for pharmacological validation of the biological pathways associated with deubiquitinase inhibition as well as starting points for the development of new therapeutics for cancer and associated disorders.

Citation Format: Tim Harrison, Xavier Jacq, Colin O'Dowd, Gerald Gavory, Oliver Barker, Christina Bell, Frank Burkamp, Stephanie Burton, Eamon Cassidy, Matthew Helm, Peter Hewitt, Natalie Page, Shane Rountree, Ewelina Rozycka, Steven Shepherd, Steven Whitehead, Mark Wappett. Targeting the ubiquitin-proteasome system by small molecule inhibition of the DUBome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-049.

Abstract 4423: Antitumor activity of the novel oral highly selective Wee1 inhibitor Debio 0123

Background: The Wee1 tyrosine kinase is activated upon DNA damage and regulates the G2-M cell cycle checkpoint. Inhibition of Wee1, in conjunction with additional genetic alterations and/or addition of a DNA damaging agent, results in mitotic catastrophe and apoptosis of cancer cells, offering an attractive approach to treating cancer. The aim of the present study was to characterize the pharmacological properties of the newly discovered, orally available, and highly selective Wee1 inhibitor Debio 0123.

Methods: Profiling of Debio 0123 was performed on 465 selected kinases in a cell-free system. Effects of Debio 0123 on downstream signaling were analyzed by ELISA and western blot in HT29 (colorectal adenocarcinoma) and A427 (lung carcinoma) cell lines. The in vitro growth inhibition activity of Debio 0123 was defined in a broad number of human cancer cell lines after 72h using a proliferation monolayer assay. Debio 0123 in vivo anti-tumoral activity was assessed in an A427 subcutaneous xenograft model in athymic nude mice. Debio 0123 pharmacodynamic effects were also evaluated after oral dosing in surrogate tissues of mice, rats and monkeys by immunohistochemistry.

Results: Debio 0123 is a highly selective ATP-competitive Wee1 inhibitor with an IC50 in the low nanomolar range. Debio 0123 inhibited Cdk1 (Cdc2) phosphorylation at Y15, a direct substrate of Wee1 in cells. Debio 0123 also induced dose- and time-dependent increased mitosis and unrepaired DNA damage shown by increased phosphorylation of histone H3 and γH2AX foci formation. In vitro activity was further studied in a large panel of cancer cell lines. Debio 0123 demonstrated submicromolar cytotoxic activity on multiple cell lines from various histotypes. In vivo, Debio 0123 was shown to inhibit phosphorylation of Cdk1 in tissues of multiple species and induction of DNA damage in a xenograft model. When administered orally once daily for 28 consecutive days, Debio 0123 induced dose-dependent anti-tumor activity and was well tolerated at all doses tested. At 30 mg/kg, treatment with Debio 0123 resulted in tumor regression.

Conclusion: Altogether these results demonstrate that Debio 0123 is a highly selective and potent Wee1 inhibitor able to prevent Cdk1 phosphorylation in multiple species and to induce apoptosis through accumulation of unrepaired DNA damage both in vitro and in vivo that result in tumor regression. The advancement of Debio 0123 into clinical studies may provide improved therapeutic outcomes for patients with cancer.

Citation Format: Colin O'Dowd, Gerald Gavory, Frank Burkamp, Adam Treder, Caroline Boyd, Tim Harrison, Frederic Massière, Astrid Glück, Christophe Chardonnens, Andrea Zaffalon, Stefania Rigotti, Robert Mader, Grégoire Vuagniaux, Anne Vaslin Chessex. Antitumor activity of the novel oral highly selective Wee1 inhibitor Debio 0123 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4423.

Abstract 1935: Accessing the cancer DUBome with UbiPlex: A bespoke drug discovery platform for deubiquitinase enzymes

Over the past decade, protein ubiquitination has emerged as an important post-translational modification with regulatory functions in all important cellular processes. Deubiquitinating enzymes (DUBs) including ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of protein substrates.

As a result of their increasing implications in the etiology of numerous pathological conditions including cancer and immuno-oncology, DUBs have emerged as an attractive and promising target class for the development of first-in-class medicines with high therapeutic impact. However, despite 15 years of intense research DUBs have proven largely refractory to drug discovery efforts.

Herein, we further describe the application of UbiPlex™, our purpose-built drug discovery platform for the identification and development of DUB inhibitors. In particular, we will highlight the versatility and robustness of UbiPlex™ by reporting the outcome of our focussed library screening campaign on multiple DUBs in parallel and by describing the de novo hit ID, orthogonal validation and hit optimization activities on two USPs of relevance to cancer.

Multiple series of novel, highly potent (e.g. IC50 < 20 nM) and non-covalent inhibitors have been developed. Excellent selectivity profiles against a large panel of DUBs and other non-related enzymes (e.g. proteases) will be described. Further profiling indicated that these inhibitors are cell-permeable and exhibit potent target engagement in cells (e.g. EC50 < 30 nM). Finally, we will describe our progress towards the development of lead molecules with drug-like properties with the aim of rapidly establishing proof-of-concept studies in vivo.

In summary, this work further exemplifies the broad tractability and druggability of the DUBome and reports the discovery and profiling of novel highly potent and selective inhibitors beyond USP7. These molecules may provide opportunities for the development of new therapeutics for cancer and associated disorders.

Citation Format: Gerald Gavory, Colin O'Dowd, Oliver Barker, Christina Bell, Frank Burkamp, Stephanie Burton, Eamon Cassidy, Joana Costa, Anthony Dossang, Matt Helm, Ashling Henderson, Peter Hewitt, Caroline Hughes, Mary McFarland, Hugues Miel, Natalie Page, Lauren Proctor, Shane Rountree, Ewelina Rozycka, Steven Shepherd, Adam Treder, Mark Wappett, Steven Whitehead, Tim Harrison. Accessing the cancer DUBome with UbiPlex: A bespoke drug discovery platform for deubiquitinase enzymes [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 1935.

Abstract 4869: Discovery and characterization of highly potent and selective USP7 inhibitors and benchmarking against clinical MDM2 antagonists

Given the importance of USP7 in known oncogenic pathways and its emerging role in immuno-oncology, the identification of USP7 inhibitors has attracted considerable interest in the scientific community. However, despite substantial efforts over the past 15 years, the development of genuine deubiquitinase (DUB) inhibitors, which exhibit both drug-like properties and a well-defined mechanism of action, has proven particularly challenging.

In this study, we report the application of UbiPlexTM, our purpose-built DUB drug discovery platform, to USP7. In particular, we detail the identification, optimization and detailed characterization of a new class of non-covalent and highly potent USP7 inhibitors (IC50 < 10 nM). In addition, these inhibitors have shown exquisite selectivity for USP7 over other DUBs and proteases. We also disclose high-resolution co-crystal structures of USP7 in complex with these inhibitors that reveal an allosteric mode of binding.

Further profiling in cells demonstrated potent target engagement with endogenous USP7 (EC50 <20 nM). In line with the known biology of USP7, this effect induced the proteasomal degradation of MDM2, concomitant stabilization of p53 and induction of p21 in multiple cell lines. The identification and parallel profiling of inactive enantiomers further validated the on-target effect of our lead molecules. Finally, we report the identification of cell lines hyper-sensitive (EC50 < 30 nM) to USP7 inhibitors in both haematological and solid cancer cell line settings and demonstrate equal or superior activity when compared to clinically relevant MDM2 antagonists.

In summary, this work exemplifies the tractability and druggability of USP7 as a cancer target and provides new insights and directions for the potential clinical development of USP7 inhibitors.

Citation Format: Gerald Gavory, Colin O'Dowd, Elias Arkoudis, Oliver Barker, Eamon Cassidy, Anthony Dossang, Jakub Flasz, Matt Helm, Caroline Hughes, Keeva McClelland, Hugues Miel, Ewa Odrzywol, Natalie Page, Tim Harrison. Discovery and characterization of highly potent and selective USP7 inhibitors and benchmarking against clinical MDM2 antagonists [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 4869.

Identification and Structure-Guided Development of Pyrimidinone Based USP7 Inhibitors

Ubiquitin specific protease 7 (USP7, HAUSP) has become an attractive target in drug discovery due to the role it plays in modulating Mdm2 levels and consequently p53. Increasing interest in USP7 is emerging due to its potential involvement in oncogenic pathways as well as possible roles in both metabolic and immune disorders in addition to viral infections. Potent, novel, and selective inhibitors of USP7 have been developed using both rational and structure-guided design enabled by high-resolution cocrystallography. Initial hits were identified via fragment-based screening, scaffold-hopping, and hybridization exercises. Two distinct subseries are described along with associated structure-activity relationship trends, as are initial efforts aimed at developing compounds suitable for in vivo experiments. Overall, these discoveries will enable further research into the wider biological role of USP7.

Identification and Characterization of Dual Inhibitors of the USP25/28 Deubiquitinating Enzyme Subfamily

The ubiquitin proteasome system is widely postulated to be a new and important field of drug discovery for the future, with the ubiquitin specific proteases (USPs) representing one of the more attractive target classes within the area. Many USPs have been linked to critical axes for therapeutic intervention, and the finding that USP28 is required for c-Myc stability suggests that USP28 inhibition may represent a novel approach to targeting this so far undruggable oncogene. Here, we describe the discovery of the first reported inhibitors of USP28, which we demonstrate are able to bind to and inhibit USP28, and while displaying a dual activity against the closest homologue USP25, these inhibitors show a high degree of selectivity over other deubiquitinases (DUBs). The utility of these compounds as valuable probes to investigate and further explore cellular DUB biology is highlighted by the demonstration of target engagement against both USP25 and USP28 in cells. Furthermore, we demonstrate that these inhibitors are able to elicit modulation of both the total levels and the half-life of the c-Myc oncoprotein in cells and also induce apoptosis and loss of cell viability in a range of cancer cell lines. We however observed a narrow therapeutic index compared to a panel of tissue-matched normal cell lines. Thus, it is hoped that these probes and data presented herein will further advance our understanding of the biology and tractability of DUBs as potential future therapeutic targets.

Discovery and characterization of highly potent and selective allosteric USP7 inhibitors

Given the importance of ubiquitin-specific protease 7 (USP7) in oncogenic pathways, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, however, the development of validated deubiquitinase (DUB) inhibitors that exhibit drug-like properties and a well-defined mechanism of action has proven particularly challenging. In this article, we describe the identification, optimization and detailed characterization of highly potent (IC₅₀ < 10 nM), selective USP7 inhibitors together with their less active, enantiomeric counterparts. We also disclose, for the first time, co-crystal structures of a human DUB enzyme complexed with small-molecule inhibitors, which reveal a previously undisclosed allosteric binding site. Finally, we report the identification of cancer cell lines hypersensitive to USP7 inhibition (EC₅₀ < 30 nM) and demonstrate equal or superior activity in these cell models compared to clinically relevant MDM2 antagonists. Overall, these findings demonstrate the tractability and druggability of DUBs, and provide important tools for additional target validation studies.

Abstract LB-319: Development and characterization of ADC999: A novel, potent orally available Wee1 inhibitor with robust antitumor efficacy in vivo

Wee1 is a tyrosine kinase that phosphorylates cyclin-dependent kinase 1 (CDC2) to inactivate the CDC2/cyclinB complex. Wee1 is therefore a key regulator of the cell cycle, maintaining the G2 checkpoint arrest to allow for pre-mitotic repair upon genomic stress. Unlike normal cells, most p53-deficient tumors lack a functional G1 checkpoint and instead rely on the G2 checkpoint for DNA repair. Abrogation of the G2 checkpoint by a Wee1 inhibitor has been shown to sensitize p53-deficient tumors to a variety of DNA-damaging anticancer agents. Strong chemosensitization has also been demonstrated in multiple pre-clinical models using targeted agents including CHK1 or PARP inhibitors. These studies combined with recent clinical data demonstrating robust anti-tumor activity in combination with carboplatin or as a single agent in tumors under high replicative stress make Wee1 a promising target for anticancer therapy. With only one inhibitor (AZD1775) in clinical development and very few reports of compounds at the preclinical stage, the development of alternative Wee1 inhibitors is of significant medical relevance. In this study, we describe the development of a novel and highly potent small molecule inhibitor of Wee1 (ADC999) and subsequent analogs. These inhibitors exhibit single digit nM IC50 values against Wee1 and good overall selectivity profiles against the kinome. In cells, target engagement was demonstrated through the inhibition of both CDC2- and CDK2-dependent Wee1 phosphorylation. In line with the mechanism of action, γH2AX and apoptosis induction was also observed in a dose-dependent manner. Further profiling in a panel of cell lines indicated strong anti-proliferative activity both in combination with cytotoxics and in monotherapy. Single agent activity was observed in multiple cancer types, including gynecological, lung and breast. In vivo, oral administration of ADC999 as a single agent led to excellent antitumor activity in a KRAS-mutant non-small cell lung carcinoma xenograft model. Responses ranged from dose-dependent tumor growth inhibition to complete and sustained regressions. ADC999 was well tolerated following a daily dosing regimen and over a prolonged period with no adverse effects observed. Evaluation of ADC999 anti-tumor activity will also be discussed in a panel of genetically-characterized patient-derived xenografts (PDXs) both as monotherapy (mini-trial design) and in combination with PARP inhibitors. In summary, we describe the development and profiling of a novel, highly potent orally available Wee1 inhibitor with robust antitumor efficacy in vivo. This inhibitor and potential back-up compounds will provide new opportunities to fully exploit the therapeutic potential of Wee1 inhibition both as standalone intervention and in combination modalities.

Citation Format: Gerald Gavory, Colin O'Dowd, Ewelina Rozycka, Caroline Boyd, Beronia Gorges, Estelle McLean, Julien Daubriac, Shane Rountree, Steven Shepherd, Stephanie Burton, Mary McFarland, Adam Treder, Andy Wilkinson, Frank Burkamp, Tim Harrison. Development and characterization of ADC999: A novel, potent orally available Wee1 inhibitor with robust antitumor efficacy in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-319. doi:10.1158/1538-7445.AM2017-LB-319

Abstract 1181: Discovery and development of novel highly potent and selective inhibitors of USP19 using UbiPlex™

Over the past decade, protein ubiquitination has emerged as an important post-translational modification with regulatory functions in all important cellular processes. Deubiquitinating enzymes (DUBs) including ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of protein substrates including tumor suppressors and oncogenes, hence regulating their levels and/or function. As a result of their increasing implications in the etiology of numerous pathological conditions including cancer, DUBs are emerging as an attractive and promising target class for the development of 1st in class medicines with high therapeutic impact. However, despite 15 years of intense research DUBs have proved largely refractory to drug discovery efforts.

Herein, we further describe the application of Ubi-Plex™, our drug discovery platform for the identification and optimisation of DUB inhibitors. In particular, we will highlight the versatility and robustness of Ubi-Plex™ by describing the outcome of our focussed library screening, hit identification, hit validation and elaboration activities on USP19.

A series of novel, highly potent (e.g. IC50 &lt; 10 nM) and reversible USP19 inhibitors have been identified. Further profiling has also demonstrated excellent selectivity against a large panel of DUBs and other non-related enzymes (e.g. kinases, proteases). These inhibitors are cell-permeable and exhibit potent target engagement in cells with EC50 values &lt; 30 nM. Finally, we will describe our progress towards the development of lead molecules with drug-like properties with the aim to rapidly establish in vivo proof-of-concept studies.

In summary, this work further exemplifies the tractability of the DUB target family and reports the discovery and detailed profiling of the first highly potent and selective inhibitors of USP19. These molecules may provide opportunities for the development of new anticancer therapeutics as well as for the treatment of muscle wasting disorders including cachexia.

Citation Format: Gerald Gavory, Colin O'Dowd, Ewelina Rozycka, Anthony Dossang, Ashling Henderson, Caroline Hughes, Hugues Miel, Oliver Barker, Joana Costa, Peter Hewitt, Mary McFarland, Lauren Proctor, Tim Harrison. Discovery and development of novel highly potent and selective inhibitors of USP19 using UbiPlex™ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1181. doi:10.1158/1538-7445.AM2017-1181

Abstract B17: Development of novel, potent orally available Wee1 inhibitors with robust antitumor efficacy in vivo

Wee1 is a tyrosine kinase that phosphorylates cyclin-dependent kinase 1 (CDC2) to inactive the CDC2/cyclinB complex. Wee1 is therefore a key regulator of the cell cycle, maintaining the G2 checkpoint arrest to allow for pre-mitotic repair upon genomic stress. Unlike normal cells, most p53-deficient tumors lack a functional G1 checkpoint and instead rely on the G2 checkpoint for DNA repair. Abrogation of the G2 checkpoint by a Wee1 inhibitor therefore sensitizes p53-deficient tumors to DNA-damaging anticancer agents and enhances their cytotoxic effect. Strong evidence for chemo-sensitization has been demonstrated in multiple pre-clinical models and also in clinical trials. These clinical observations combined with recent reports demonstrating single agent efficacy make Wee1 a promising target for anticancer therapy. With only one inhibitor (AZD1775) in clinical development and very few reports of compounds at the preclinical stage, the development of alternative Wee1 inhibitors is of significant medical relevance.

In this study, we describe the development of novel and highly potent small molecule inhibitors of Wee1 emanating from 2 distinct chemical series (ADC730, ADC999). These inhibitors exhibit single digit nM IC50 values versus the enzyme and good selectivity profiles against the kinome. In cells, target engagement was demonstrated through the inhibition of both CDC2- and CDK2-dependent Wee1 phosphorylation. In line with the mechanism of action, gH2AX and apoptosis induction was also observed in a dose-dependent manner. Further profiling in panels of cell lines indicated strong anti-proliferative activity both in combination with cytotoxics (i.e. gemcitabine) and in monotherapy. Single agent activity was observed in multiple cancer types, including gynecological, lung, colorectal and breast.

In vivo, oral administration of ADC730 in combination with gemcitabine resulted in significant dose-dependent growth reduction in a HT29 tumor xenograft model and the combination was synergistic. Dosed orally and as single agents, both ADC730 and ADC999 also demonstrated excellent antitumor activity in the A427 KRAS-mutant lung carcinoma xenograft model. Responses ranged from dose-dependent tumor growth inhibition to complete regressions. ADC730 and ADC999 were well tolerated in these studies with no signs of adverse effects observed.

In summary, we describe the development and profiling of novel, highly potent orally available Wee1 inhibitors with robust antitumor efficacy in vivo. These inhibitors will provide new opportunities to fully exploit the therapeutic potential of Wee1 inhibition, either as standalone intervention or in combination modalities.

Citation Format: Gerald Gavory, Colin O'Dowd, Ewelina Rozycka, Caroline Boyd, Beronia Gorges, Estelle McLean, Shane Rountree, Steven Sheperd, Stephanie Burton, Mary McFarland, Dominic Janssen, Adam Treder, Andy Wilkinson, Frank Burkamp, Tim Harrison. Development of novel, potent orally available Wee1 inhibitors with robust antitumor efficacy in vivo [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr B17.

Abstract LB-159: A novel, potent and selective inhibitor of Wee1 with robust antitumor activity in various cancer xenograph models

Wee1 is a tyrosine kinase that phosphorylates cyclin-dependent kinase 1 (CDK1/CDC2) to inactive the CDC2/cyclinB complex. Wee1 is therefore a key regulator of the cell cycle, maintaining the G2 checkpoint arrest to allow for premitotic repair in case of DNA damage. Unlike normal cells, most p53-deficient tumors lack a functional G1 checkpoint and instead rely on the G2 checkpoint for DNA repair. Abrogation of the G2 checkpoint by a Wee1 inhibitor may therefore sensitize p53-deficient tumors to DNA-damaging anticancer agents and enhance their cytotoxic effect. Strong evidence for chemo-sensitization has been demonstrated from multiple pre-clinical models and also from clinical trials. In particular, treatment in combination with carboplatin recently showed encouraging antitumor activity in patients with p53-mutated ovarian cancer refractory or resistant to standard first-line therapy. These clinical observations combined with recent reports demonstrating single agent efficacy in specific contexts make Wee1 a promising target for anticancer therapy. With only one inhibitor in clinical development (AZD1775) and very limited reports at the preclinical stage, the development of alternative, novel Wee1 inhibitors may have significant therapeutic value.

In this study, we describe the development and characterization of ADC730, a potent and highly selective small molecule Wee1 inhibitor. ADC730 inhibits Wee1 kinase activity with an IC50 of &lt;5 nM and demonstrates excellent selectivity when profiled against a diverse panel of kinases. In cellular assays, ADC730 potently inhibited CDC2-dependent Wee1 phosphorylation. Further studies in a panel of cancer cell lines demonstrated strong anti-proliferative activity of ADC730 both in combination with gemcitabine or in monotherapy modalities. Single agent activity was observed in multiple cancer types including lung and kidney. gH2AX foci formation followed by apoptosis induction were typically observed in a dose-dependent manner for the most sensitive cell lines.

In vivo, oral administration of ADC730 (10, 30 mg/kg/day) in combination with gemcitabine caused a significant dose-dependent growth reduction of HT29 tumors and the combination was synergistic. ADC730 was well tolerated in all cases with no signs of adverse effects. Dosed orally as a single agent (10, 30 mg/kg/day), ADC730 also demonstrated robust dose-dependent anti-tumor efficacy in the A427 lung carcinoma model with inhibition of tumor growth consistent with the pharmacodynamic modulation of Wee1 signaling. In comparison and under similar experimental conditions, AZD1775 demonstrated similar efficacy profiles at significantly higher doses.

To conclude, we describe the development and profiling towards candidate nomination of ADC730, a novel potent highly selective Wee1 inhibitor with robust efficacy in cancer xenograft models both in combination and single agent modalities. Subsequent analogs and examples with potentially enhanced profiles will also be described.

Citation Format: Gerald Gavory, Colin O’Dowd, Frank Burkamp, Shane Rountree, Ewelina Rozycka, Caroline Boyd, Beronia Gorges, Stephanie Burton, Andy Wilkinson, Steven Shepherd, Dominic Janssen, Mary McFarland, Shane Rountree, Tim Harrison. A novel, potent and selective inhibitor of Wee1 with robust antitumor activity in various cancer xenograph models. [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 LB-159.

Abstract LB-257: Discovery and characterization of novel, highly potent and selective USP7 inhibitors

Over the past decade, protein ubiquitination has emerged as an important post-translational modification with roles in a plethora of cellular processes, and dysregulation in the ubiquitin proteasome system pathway (UPS) has been implicated in multiple human disorders including cancer.

Ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of numerous protein substrates including tumor suppressors and oncogenes, hence regulating their levels and/or functions. USPs therefore represent a fast growing and attractive target class for pharmacological intervention. USP7 in particular has attracted considerable attention for its implications in multiple key oncogenic pathways including most notably MDM2/p53, PTEN and DNA damage.

As part of a focussed effort towards targeting USPs, fragment screening was performed against a panel of family members, including USP7. Hits were identified by surface plasmon resonance and validated using orthogonal biophysical techniques (NMR, thermophoresis). Subsequent hit expansion identified molecules for which high-resolution co-crystal structures have been solved providing unique opportunities for structure-based design.

Medicinal chemistry optimisation has yielded a series of novel, reversible and potent USP7 inhibitors (e.g. IC50 &lt; 10 nM) with excellent selectivity profiles against deubiquitinating (DUBs) and other non-related enzymes. These inhibitors are cell-permeable and also exhibit potent target engagement in cells (e.g. EC50 &lt; 30 nM). In line with the mechanism of action, further cellular profiling has demonstrated effects on p53, p21 and MDM2 levels in a concentration-dependant manner. From a translational viewpoint, initial studies aimed at identifying cell lines sensitive to these inhibitors will also be discussed.

In summary, we report the discovery and detailed biochemical and cellular profiling of novel, potent and selective inhibitors of USP7. These molecules have drug-like properties and may provide opportunities for the development of new anticancer therapeutics.

Citation Format: Gerald Gavory, Colin O'dowd, Keeva McClelland, Ewa Odrzywol, Alan Brown, Stephanie Burton, Oliver Barker, Frank Burkamp, Matt Helm, Iain James, Jakub Flasz, Elias Arkoudis, Tim Harrison. Discovery and characterization of novel, highly potent and selective USP7 inhibitors. [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 LB-257. doi:10.1158/1538-7445.AM2015-LB-257