First-in-Class Targeted Protein Degrader of MLLT1/3 for the Treatment of Advanced AML and ALL Including Menin Inhibitor Resistant / Refractory Disease

Background: MLLT-1 and -3 are two highly homologous histone reader proteins that are critical mediators of the Super Elongation Complex (SEC), a developmental transcriptional regulator. The SEC, which is commonly hijacked in cancer, promotes RNA Polymerase II dependent transcription of major oncogenes and tumor drivers e.g., MYC, BCL2, CDK6, HOXA9 and MEIS1. SEC-dependent transcription is a recognized driver in multiple AML and ALL sub-populations, such as those defined by KMT2A-rearrangements (KMT2Ar) and NPM1 mutations (NPM1m). Clinical proof-of-concept for targeting the SEC has recently been demonstrated with inhibitors of menin, a protein associated with the SEC in some dependent cancers. However, many patients do not respond to, or rapidly progress on menin-inhibitors. Hence there is a high need for additional therapies that can broadly target SEC dependent cancers including those that are resistant to menin-inhibitors.

Targeting MLLT1/3 represents a novel therapeutic approach to blocking the SEC and inhibitors of MLLT1/3 histone reader function have been shown to have anti-cancer activity in a range of AML and ALL cell model systems. In this presentation we will describe the discovery of a first-in-class targeted protein degrader (TPD) of MLLT1/3 that has a markedly improved pharmacological profile vs MLLT1/3 inhibition and a differentiated profile vs menin-inhibition. This encompasses potent activity across a wide range of AML and ALL model systems including those that are resistant to menin-inhibitors.

Methods: Targeted degradation of MLLT1/3 was assessed using the Jess Simple Western system. MLLT target gene expression was measured by qPCR in leukemia cell lines. The anti-proliferative potential of MLLT1/3 targeted agents was assessed across a broad range of leukemic and normal cell lines and compared with menin inhibitors and other standard of care compounds using a cell viability readout. Combination studies were performed in leukemia cell lines with MLLT1/3 targeted agents, venetoclax and menin inhibitors. The clonogenic potential of MLLT1/3 targeted agents was determined using colony formation assays. Apoptosis was measured using caspase 3/7 readout. In vivo activity was assessed in a MV4-11 subcutaneous model.

Results: We have identified a novel and selective TPD of MLLT1/3, based on a highly selective YEATS domain binding small molecule inhibitor, that led to rapid and potent degradation of mouse and human MLLT1/3 with DC₅₀ values <1nM. This compound blocked SEC mediated gene transcription of multiple oncogenes including MYC and MYB. In leukemic model cell systems, the MLLT1/3 TPD potently induced apoptosis or terminal differentiation, and blocked clonogenic potential of the cancer cells with minimal impact against non-cancer cells. In head-to-head studies the MLLT1/3 TPD provided markedly more potent and broader anti-cancer activity across a panel of AML and ALL cells than the MLLT1/3 inhibitor and a clinical menin-inhibitor. This included benefit in KMT2Ar and NPM1m driven leukemia cell lines, and in cell lines with other driver events not sensitive to menin-inhibition. Notably, the MLLT1/3 TPD was highly active against AML cells engineered to express clinically relevant drug-resistant menin-mutations. Furthermore, the MLLT1/3 TPD showed synergistic anti-cancer activity when combined with standard-of-care agents such as venetoclax and with menin inhibitors. In an in vivo MV4-11 xenograft model the MLLT1/3 TPD degraded MLLT1 protein, downregulated SEC target gene transcription and blocked tumour growth at well tolerated oral doses, with no evidence of hematological toxicity.

Conclusion: Targeting MLLT1/3 with a TPD is an attractive approach with potential as a single agent across a broad range of molecularly defined acute leukemias. Notably, marked activity in menin-resistant leukemic cell models was observed, supporting the potential to treat patients refractory to, or who progress on, menin-inhibitors: a high unmet clinical need. Finally, beneficial combinations with clinically relevant agents support the potential for a MLLT1/3 TPD to be used as part of early line standard-of-care treatment in AML and ALL.