Abstract Using our QuEENTM molecular glue degrader (MGD) discovery engine that integrates biochemical and cellular assays with in silico modeling, we identified and optimized MGDs that induce proteasomal degradation of cyclin E1 (CCNE1) as a therapeutic strategy for CCNE1-amplified cancers. We generated a highly selective CCNE1 degrader that spares related cyclins and other proteins. CCNE1 is a key regulator of G1/S cell-cycle progression. As the regulatory subunit of the CCNE1–CDK2 holoenzyme, it promotes RB phosphorylation, relieves RB-mediated repression, and drives proliferation. CCNE1 is frequently amplified and/or overexpressed across multiple tumor types (including ovarian, endometrial, gastric, and breast cancers), making it an attractive therapeutic target. However, as a non-enzymatic regulatory protein, CCNE1 has been considered difficult to drug with conventional approaches. Our CCNE1 MGD selectively inhibited proliferation of CCNE1-amplified cancer cell lines while sparing non-amplified lines, consistent with the hypothesis that CCNE1 amplification is an indication of oncogene addiction. The antiproliferative phenotype was accompanied by markedly reduced RB phosphorylation and suppression of E2F-driven transcription, supporting an on-target mechanism of action. In addition, we observed strong induction of senescence markers in CCNE1 MGD-treated cells, indicating an exit from the cell cycle. In in vivo studies, orally dosed CCNE1 MGD produced robust tumor growth inhibition and regression as monotherapy in CCNE1-amplified ovarian, breast, and gastric models. Multiple CDK2 kinase inhibitors are in clinical development for CCNE1-amplified cancers. Through kinome profiling and genetic modeling, we found that clinical-stage CDK2 inhibitors can exhibit substantial off-target activity, highlighting the differentiated selectivity profile of the CCNE1 MGD and supporting the potential for improved tolerability versus less selective CDK2 inhibition. To model potential CCNE1 MGD and CDK2 inhibitor toxicity in vitro, we conducted colony-forming unit (CFU) assays with normal human erythroid and myeloid progenitor cells. While CDK2 inhibitors reduced both erythroid and myeloid colony formation, our CCNE1 MGD had no effect on either lineage, further supporting their potential for superior tolerability. These observations are in line with the recently completed dose-range finding toxicology studies for our CCNE1 MGD in rats and cynomolgus monkeys, where no adverse events were noted, as shown by in-life observations, histopathology, and clinical chemistry. In conclusion, CCNE1 MGD provides a first-in-class approach to directly target a frequently amplified, non-enzymatic driver oncogene and represents a differentiated precision medicine strategy for patients with CCNE1-altered cancers. Citation Format: William Tahaney, Yimao Liu, Ahmed Abdullah, Vittoria Massafra, Verena Lang, Markus Baumann, Aurelie Dubois, Arnaud Osmont, Xavier Lucas, Chao Quan, Anna Kostikova, Anna Diesslin, Freya Harvey, Christelle Bianda, Kevin Larpenteur, Katherine Jones, Anne-Cecile D’Alessandro, Carolina Perdomo Ortiz, Herve Farine, Maciej Cabanski, Manav Korpal, Bradley Demarco, Debora Bonenfant, Markus Warmuth, Filip Janku, Magnus Walter, Sharon Townson, Bernhard Fasching, Simone Tortoioli, Chris King, Laura McAllister, Sofia Gkountela, Beatrice Ranieri, Ralph Tiedt, Nina Ilic-Widlund. Targeting the “undruggable” oncogene CCNE1 using a molecular glue degrader in CCNE1 amplified cancers [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr B044.

Abstract Cyclin E1 (CCNE1) is a critical driver of cell cycle progression and cell proliferation. It acts as the regulatory subunit for the CCNE1-CDK2 holoenzyme, which coordinates cell cycle progression through the G1/S phases and effectively drives cell proliferation via RB phosphorylation and repression. CCNE1 is frequently amplified or overexpressed across multiple cancer types, including ovarian, endometrial, gastric, breast, and others, and thus pharmacological targeting of CCNE1 is expected to benefit patients whose cancers bear these alterations. Despite the clear therapeutic promise of directly targeting CCNE1 in these patients, CCNE1 has been considered undruggable by conventional means as it is a regulatory non-enzymatic protein. Hence, we sought to identify molecular glue degraders (MGDs) that selectively target CCNE1 for proteasomal degradation. Using our MGD discovery engine QuEENTM encompassing biochemical and cellular assays as well as in silico modelling, we identified and optimized molecules that potently degrade CCNE1. Leveraging a cryptic pocket, our CCNE1 MGDs selectively degrade the cyclin E1/CDK2 holoenzyme complex, while sparing other proteins such as closely related cyclins or CDKs. In CCNE1 amplified cancer cell lines CCNE1 MGDs selectively inhibit cellular proliferation, while sparing cell lines without amplification, in line with the “oncogenic addiction” paradigm. These anti-proliferative effects were determined to be governed by downmodulation of RB phosphorylation and E2F-driven gene expression, attesting to the on-target function of our CCNE1 MGDs. When assessed in vivo, orally dosed CCNE1 MGDs induced robust tumor growth suppression and regression as a monotherapy in CCNE1 amplified ovarian, breast, and gastric models. We further established that clinical stage CDK2 inhibitors exhibit significant off-target activity through kinome profiling and genetic modeling, demonstrating the superior selectivity of CCNE1 MGDs. Owing to their exquisite selectivity, we expect that CCNE1 MGDs will avoid dose-limiting toxicities associated with less selective CDK2 inhibitors. CCNE1 MGDs represent a first in class opportunity and a paradigm shift due to their ability to directly target a frequently amplified non-enzymatic driver oncogene in distinct populations of cancer patients with high unmet medical need. With their distinctive ability to spare other proteins whose inhibition is associated with dose-limiting toxicities, CCNE1 MGDs offer a unique precision medicine angle for populations in desperate need of treatment options. Citation Format: William Tahaney, Yimao Liu, Ahmed Abdullah, Vittoria Massafra, Verena Lang, Markus Baumann, Aurelie Dubois, Arnaud Osmont, Xavier Lucas, Chao Quan, Anna Kostikova, Anna Diesslin, Freya Harvey, Christelle Bianda, Kevin Larpenteur, Katherine Jones, Anne-Cecile D’Alessandro, Carolina Perdomo Ortiz, Herve Farine, Maciej Cabanski, Manav Korpal, Bradley Demarco, Debora Bonenfant, Markus Warmuth, Filip Janku, Magnus Walter, Sharon Townson, Bernhard Fasching, Simone Totoioli, Christopher King, Laura McAllister, Beatrice Ranieri, Sofia Gkountela, Ralph Tiedt, Nina Ilic Widlund. Selective targeting of CCNE1 using molecular glue degraders for the treatment of CCNE1 amplified cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6778.

The CRL4 CRBN E3 ubiquitin ligase is the target of molecular glue degrader compounds that reprogram ligase specificity to induce the degradation of clinically relevant neosubstrate proteins. Known cereblon (CRBN) neosubstrates share a generalizable β-hairpin G-loop recognition motif that allows for the systematic exploration of the CRBN target space. Computational mining approaches using structure- and surface-based matchmaking algorithms predict more than 1600 CRBN-compatible G-loop proteins across the human proteome, including the newly discovered helical G-loop motif, and identify the noncanonical neosubstrate binding mode of VAV1 that engages CRBN through a molecular surface mimicry mechanism. This work broadens the CRBN target space, redefines rules for neosubstrate recognition, and establishes a platform for the elimination of challenging drug targets by repurposing CRL4 CRBN through next-generation molecular glue degraders.

Cyclin dependent kinases 4 and 6 (CDK4 and CDK6) and cyclin dependent kinase 2 (CDK2) act sequentially to coordinate cell cycle progression through the G1/S phases and effectively drive cell proliferation via RB phosphorylation and repression. CDK4/6 inhibitors in combination with endocrine therapy are approved agents for the treatment of hormone-receptor (HR)-positive/HER2-negative breast cancer. While these agents offer substantial benefit, patients eventually relapse. It has been reported that approximately 30% of resistant tumors following CDK4/6 inhibitor treatment exhibit upregulation of CCNE1 expression, and others are thought to adapt to chronic CDK4/6-inhibition by increased tumor reliance on the CDK2 pathway to sustain downstream signaling along the RB-E2F axis. Hence, targeting CDK2 in conjunction with CDK4/6 inhibition is expected to provide more sustained responses in this difficult-to-treat patient population. We sought to identify molecular glue degraders (MGDs) that selectively target CDK2. Using our MGD discovery engine QuEENTM encompassing biochemical and cellular assays as well as in silico modelling, we identified and further optimized molecules that induce CRBN engagement and selective degradation of CDK2, while sparing other proteins such as closely related CDKs. Unlike CDK2 inhibitors, CDK2 MGD inhibits cell proliferation in an RB-dependent manner, attesting to its superior selectivity. Furthermore, this MGD induces robust downstream pathway suppression, as evidenced by downmodulation of RB phosphorylation and E2F-driven gene expression. When dosed orally in preclinical models of HR-positive/HER2-negative breast cancer, this compound drives deep tumor regression in combination with CDK4/6 inhibitor or triple combination with endocrine therapy (fulvestrant), resulting in enhanced downstream pathway suppression compared to CDK4/6 inhibitor alone. Owing to its superior selectivity, we expect that a CDK2 MGD will avoid dose-limiting toxicities associated with less selective CDK2 inhibitors. Hence, a CDK2 MGD provides novel means to target an inadequately drugged target, offering a unique angle for populations in desperate need of treatment options. Citation Format: Nina Ilic-Widlund, William Tahaney, Vasia Vafeiadou, Christelle Bianda, Liam Cheeseman, Ambika Singh, Anna Diesslin, Sophia Nguyen, Luca Moccia, Christopher King, Yimao Liu, Chao Quan, Xavi Lucas, Vladas Oleinikovas, Bradley Demarco, Laura Schwander, Vaik Strande, Jessica Alers, Rajiv Narayan, Dave Peck, Sarah Pessa, Samuel Gilberto, John Castle, Sharon Townson, Markus Warmuth, Magnus Walter, Ralph Tiedt, Andreas Ritzen, Beatrice Ranieri, Sofia Gkountela. Selective Targeting of CDK2 Using Molecular Glue Degraders for the Treatment of HR-Positive/HER2-Negative Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P5-01-26.

Cyclin dependent kinases 4 and 6 (CDK4 and CDK6) and cyclin dependent kinase 2 (CDK2) act in a coordinated fashion to phosphorylate and repress RB protein, effectively driving cell proliferation via E2F activation. Currently, CDK4/6 inhibitors in combination with endocrine therapy are considered the standard of care for the treatment of hormone-receptor (HR)-positive/HER2-negative breast cancer, but unfortunately most patients with metastatic disease ultimately progress. High CCNE1 expression is considered one of the underlying mechanisms of resistance to CDK4/6-inhibition, and other adaptations to chronic CDK4/6-inhibition that increase reliance on the CDK2 pathway to sustain RB-E2F signaling are also thought to reduce CDK4/6 inhibitor effectiveness. Based on this, we reason that, targeting CDK2 in conjunction with CDK4/6 inhibition can provide more sustained and durable responses in this difficult-to-treat patient population. To identify molecular glue degraders (MGDs) that selectively target CDK2, we used our MGD discovery engine QuEENTM. Through this platform that encompasses biochemical and cellular assays as well as in silico modelling, we identified and further optimized molecules that induce CRBN engagement to drive selective CDK2 degradation. Unlike CDK2 inhibitors, our CDK2 MGDs spare other proteins such as closely related CDKs and, attesting to their superior selectivity, inhibit cell proliferation in an RB-dependent manner. Furthermore, these MGDs induce robust downstream pathway suppression, as evidenced by downmodulation of RB phosphorylation and E2F-driven gene expression. When dosed orally in in vivo models of HR-positive/HER2-negative breast cancer, these compounds drive deep tumor regression in combination with CDK4/6 inhibitor or triple combination with endocrine therapy (fulvestrant), resulting in enhanced downstream pathway suppression compared to CDK4/6 inhibitor alone. Owing to their superior selectivity, we expect that a CDK2 MGDs will avoid dose-limiting toxicities associated with less selective CDK2 inhibitors. Hence, CDK2 MGDs provide novel means to target an inadequately drugged target, offering a unique angle for populations in desperate need of treatment options. Sofia Gkountela, William Tahaney, Vasiliki Vafeiadou, Christelle Bianda, Liam Cheeseman, Ambika Singh, Anna Diesslin, Martin Schillo, Sophia Nguyen, Luca Moccia, Christopher King, Yimao Liu, Chao Quan, Bradley DeMarco, Laura Schwander, Vaik Strande, Jessica Alers, Rajiv Narayan, Dave Peck, Sarah Pessa, Samuel Gilberto, John Castle, Filip Janku, Sharon Townson, Markus Warmuth, Magnus Walter, Beatrice Ranieri, Ralph Tiedt, Nina Ilic Widlund. Selective targeting of CDK2 using molecular glue degraders for the treatment of HR-positive/HER2-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB422.

Abstract We have previously described our GSPT1 molecular glue degrader MRT-2359, which was optimized to achieve preferential antiproliferative activity in non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) expressing high N-MYC or L-MYC mRNA. A clinical trial with this new drug candidate is ongoing (NCT05546268). Here, we present pre-clinical profiling of MRT-2359 across hundreds of cancer cell lines representing multiple cancer types, aiming at identifying other cancers where preferential sensitivity is associated with high expression of a MYC family member. These studies showed that prostate cancer cell lines clearly segregate into groups that are either sensitive or insensitive. Sensitive prostate cancer cell lines could be further divided into two subgroups: (1) androgen receptor positive cell lines displaying higher c-MYC mRNA expression levels than the other prostate cancer cell lines, (2) neuroendocrine prostate cancer cell lines with or without high N-MYC. The latter is in line with our previous observation that the neuroendocrine phenotype is generally associated with heightened sensitivity to MRT-2359 independently of MYC status. The insensitive cell lines were androgen receptor and neuroendocrine negative and displayed lower c-MYC mRNA levels. GSPT1 degradation in androgen receptor-positive cell lines led to rapid and deep loss of c-MYC protein as well as reduction of androgen receptor, including the splice variant AR-V7 that is associated with resistance to agents targeting androgen signaling. In androgen receptor-negative cell lines, the levels of c-MYC protein decreased only modestly upon GSPT1 degradation. Finally, in immunocompromised mice, xenografts of the AR-V7-positive cell line 22RV1 and the neuroendocrine prostate cell line NCI-H660, both of which are sensitive to MRT-2359 in vitro, were treated with several MRT-2359 dose regimens including continuous as well as intermittent (5 days on/9 days off) dosing. Most regimens led to marked tumor regression. Tumors of both models fully regressed after a 4-week course of 10 mg/kg MRT-2359 once daily, and no tumor regrowth could be detected after cessation of treatment. No significant in vivo response was observed for xenografts of the insensitive cell line PC-3. These data support the clinical investigation of MRT-2359 in prostate cancer. Citation Format: Ralph Tiedt, Martin Schillo, Arnaud Osmont, Débora Bonenfant, Rajiv Narayan, Owen Wallace, Markus Warmuth. The GSPT1 molecular glue degrader MRT-2359 is active against prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3294.

H3B-5942 suppresses co-activator recruitment and shows potency in endocrine sensitive and resistant lines

Crystallographic Data collection and Refinement Statistics.

Supplementary Figures 1-13 from The Polycomb Group Protein Bmi-1 Is Essential for the Growth of Multiple Myeloma Cells

Supplementary Table 1 from The Polycomb Group Protein Bmi-1 Is Essential for the Growth of Multiple Myeloma Cells

H3B-6527 efficacy studies in 30 PDX models show that 10 models are responsive

Abstract MYC transcription factors have been demonstrated to be drivers of many cancers, yet have remained recalcitrant to new drug development. We hypothesized that MYC-driven cancer cell lines are addicted to protein translation, and therefore are vulnerable to the loss of the translation termination factor, GSPT1. We have discovered MRT-2359, a selective GSPT1 molecular glue degrader, that demonstrates potent 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. MRT-2359 has been optimized for differential toxicity between MYC- and non-MYC-driven cancer cell lines, kinetics and depth of degradation, oral bioavailability, and in vivo efficacy. The anti-tumor activity of MRT-2359 was assessed in more than 80 lung patient-derived xenografts (PDXs) that confirmed the preferential anti-tumor activity in N- and L-MYC high NSCLC and SCLC PDXs when dosed orally daily or intermittently. Similar levels of activity were also observed in neuroendocrine lung cancer PDXs and lymphoma models. 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: Owen B. Wallace, 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, Markus Warmuth, Filip Janku, Bernhard Fasching. Discovery of MRT-2359, an orally bioavailable GSPT1 molecular glue degrader, for MYC-driven cancers [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 ND10.

Legends describing each of the supplementary figures and tables

Supplementary Table 1 from The ITK-SYK Fusion Oncogene Induces a T-Cell Lymphoproliferative Disease in Mice Mimicking Human Disease

H3B-5942 exhibits dose-dependent inhibition of ER target genes and shows significant efficacy ER Wt and mutant in vivo models

Body weight data of H3B-6527 as single agent and in combination

H3B-6527 response in 40 HCC cell lines and 625 cell lines.

Supplemental Methods and Materials, Supplementary Figures 1-12, Supplementary Figure Legends from Protein Kinase C Inhibitor Sotrastaurin Selectively Inhibits the Growth of CD79 Mutant Diffuse Large B-Cell Lymphomas