METHODS OF TREATING ACUTE LEUKEMIA

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application No. 63/382,084, filed on November 2, 2022, U.S. Provisional Application No. 63/386,649, filed on December 8, 2022, U.S. Provisional Application No. 63/497,125, filed on April 19, 2023, and U.S. Provisional Application No. 63/504,995, filed on May 30, 2023, each of which is incorporated herein by reference in its entirety.

BACKGROUND

[0002] Acute leukemia is a group of blood cancers characterized by a rapid increase in the number of immature blood cells, and includes acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL). AML is a diverse group of highly fatal blood cancers and is characterized by the proliferation of myeloid precursors (myeloid blasts or progranulocytes) that fail to undergo normal differentiation. AML develops as the consequence of a series of genetic changes in a hematopoietic precursor cell. These changes alter normal hematopoietic growth and differentiation, resulting in an abnormal accumulation of large numbers of these immature myeloid blasts in the bone marrow in peripheral blood, which, in turn, interfere with production of normal blood cells. As with other malignancies, genetic alterations in AML include mutation of oncogenes as well as the loss of tumor suppressor genes. In contrast to most solid tumors, however, many hematologic malignancies are associated with a single characteristic cytogenetic abnormality. This clinically heterogeneous disease is characterized by a multitude of chromosomal abnormalities and gene mutations, which translate to marked differences in responses and survival following chemotherapy, and significant challenges for successful and durable AML treatment. (Kumar, C.C., Genes Cancer 2011, 2(2), 95-107.) Analogously, ALL involves genetic changes that lead to creating of leukemic lymphoblasts in the bone marrow that impact production of new red blood cells, white blood cells, and platelets. ALL is the most common type of leukemia in young children, and the most common cause of death from cancer in children. While most cases of ALL occur in children, 80% of deaths from ALL occur in adults. SUMMARY

[0003] Provided and described herein are methods of treating acute leukemia, such as acute myeloid leukemia (AML) or acute lymphocytic leukemia (ALL), in an individual, or of inhibiting proliferation and/or inducing apoptosis in a leukemia cell in an individual, wherein the acute leukemia or leukemia cell comprises a nucleophosmin 1 (NPM1) mutation, a lysine methyltransferase 2a (KMT2A) rearrangement, a SET domain containing 2 (SETD2) mutation, or a runt-related transcription factor 1 (RUNX1) mutation, comprising administering to the individual 600 milligrams daily of ziftomenib, or an isotopolog thereof, or a pharmaceutically acceptable salt or such compound or isotopolog, or a solvate of any of the foregoing (collectively, “ziftomenib, or a pharmaceutically acceptable form thereof’), or a pharmaceutical composition comprising ziftomenib or a pharmaceutically acceptable form thereof. In some aspects, the acute leukemia is menin-dependent. In some aspects, the acute leukemia or leukemia cell comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-internal tandem duplication (ITD) mutation or a FLT3 mutation in the tyrosine kinase domain (FLT3-TKD mutation)) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof. As described herein, ziftomenib, dosed at 600 milligrams daily, demonstrates significant clinical efficacy in acute leukemia, as shown by the rate of clinical responses, coupled with a manageable safety and tolerability profile, particularly when administered to individuals with specific genetic anomalies, including NPM1 mutations or KMT2A rearrangements. Also provided and described herein are methods of treating acute leukemia, such as AML or ALL, in an individual, or of inhibiting proliferation and/or inducing apoptosis in a leukemia cell in an individual, wherein the acute leukemia is a menin-dependent leukemia, optionally wherein the leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A partial tandem duplication (KMT2A-PTD), a SETD2 mutation, a RUNXl mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, comprising administering to the individual 600 mg of ziftomenib or a pharmaceutically acceptable form thereof, or a pharmaceutical composition comprising ziftomenib or a pharmaceutically acceptable form thereof daily. In some aspects, the acute leukemia comprises anNPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof. [0004] Provided herein are methods of treating extramedullary leukemia in an individual with acute leukemia comprising administering a therapeutically effective amount of a menin inhibitor, in particular 600 milligrams of ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual, optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation. Extramedullary leukemia is characterized by the presence of leukemic cell aggregates outside the bone marrow medullary cavity, optionally in the form of a solid tumor of myeloblasts. In some aspects, the extramedullary leukemia is menin-dependent. Also provided and described herein are methods of treating extramedullary leukemia in an individual with acute leukemia, wherein the acute leukemia is a menin-dependent leukemia, optionally wherein the leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, aRUNX1 mutation, aFLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, comprising administering to the individual 600 milligrams daily of ziftomenib or a pharmaceutically acceptable form thereof, or a pharmaceutical composition comprising ziftomenib or a pharmaceutically acceptable form thereof. In some aspects, the extramedullary leukemia comprises an NPM1 mutation, optionally in combination with aFLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof. In some aspects, the acute leukemia is AML or ALL.

[0005] Also provided herein are methods of increasing the level of myeloid blasts in the blood of an individual with AML comprising administering a therapeutically effective amount of a menin inhibitor, in particular 600 mg of ziftomenib or a pharmaceutically acceptable form thereof, daily to the individual, wherein the AML optionally comprises an NPM1 mutation, a KMT2A rearrangement, an SETD2 mutation, or a RUNX1 mutation. Ziftomenib has been observed to generate a significant and steady increase in the level of blasts in blood, a situation that usually indicates leukemic disease progression. However, for ziftomenib, blast liberation from bone marrow into intramedullary space has been discovered to correlate with sensitivity of the leukemia to ziftomenib therapy and in such cases this effect is not indicative of disease progression. In some embodiments, the AML is menin-dependent. In some embodiments, the AML comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof. In some aspects, the AML comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-internal tandem duplication (ITD) mutation or a FLT3 mutation in the tyrosine kinase domain (FLT3-TKD mutation)) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof. The increase in the levels of myeloid blasts can be transient and can be followed by a reduction in myeloid blasts in the blood.

[0006] Also provided herein are methods of identifying an acute leukemia in an individual as sensitive to administration of a menin inhibitor, in particular ziftomenib, comprising: administering an effective amount of the menin inhibitor, in particular 600 mg ziftomenib or a pharmaceutically acceptable form thereof to the individual daily, receiving an identification of the level of myeloid blasts in a first blood sample taken from the individual at a first timepoint that is either before initiation of the administering or during the administering, receiving an identification of the level of myeloid blasts in a second blood sample taken from the individual at a second timepoint that is after the first timepoint and that is during the administering, and determining that the acute leukemia is sensitive to the administering if the level of myeloid blasts at the second timepoint is greater than the level at the first timepoint, optionally wherein the acute leukemia is menin-dependent, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3-VXD mutation or a FLT3- TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably wherein the acute leukemia comprises an NPM1 mutation or a KMT2A rearrangement.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0007] Also provided herein are methods of treating a differentiation disorder in an individual diagnosed with the differentiation disorder and with acute leukemia, or reducing the risk of developing a severe differentiation disorder in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A -PTD mutation, aSETD2 mutation, a RUN X1 mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably wherein the acute leukemia comprises an NPM1 mutation or a KMT2A rearrangement, comprising:

(a) administering a therapeutically effective amount of a menin inhibitor, in particular 600 mg of ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual,

(b) administering IV hydration to the individual, and optionally,

(c) administering an effective amount of a xanthine oxidase inhibitor to the individual, optionally wherein the xanthine oxidase inhibitor is allopurinol, optionally administering the allopurinol at a dose of about 200-400 mg/m ² /day in 1-3 divided doses, up to a maximum of about 800 mg daily.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0008] Also provided herein are methods of treating a differentiation disorder in an individual with acute leukemia, or reducing the risk of developing a severe differentiation disorder in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent or wherein the acute leukemia comprises NPM1 mutation, a KMT2A rearrangement, a KMT2A -PTD mutation, a SETD2 mutation, aRUNX1 mutation, aFLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably an NPM1 mutation or a KMT2A rearrangement, comprising:

(a) administering an effective amount of a menin inhibitor, in particular 600 mg of ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual,

(b) administering IV hydration to the individual, and (c) administering a therapeutically effective amount of rasburicase, optionally at a dose of about 0.2 mg/kg, optionally as an intravenous infusion over about 30 minutes daily, for up to about 5 days.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0009] Also provided are methods of treating a differentiation disorder, or reducing the risk of developing a severe differentiation disorder, in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent, or wherein the acute leukemia comprises NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably an NPM1 mutation or a KMT2A rearrangement, comprising:

(a) administering a prophylactic and/or effective amount of a corticosteroid to the individual, optionally wherein the corticosteroid is prednisone, optionally at a dose of about 0.5 mg/kg (or an equivalent dose of an alternative corticosteroid); and

(b) administering a therapeutically effective amount of a menin inhibitor to the individual.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0010] Also provided herein are methods of reducing transfusion dependence in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent, or wherein the acute leukemia comprises an NPM1 mutation, a. KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3- TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably an NPM1 mutation or a. KMT2A rearrangement, comprising administering to the individual 600 milligrams daily of ziftomenib, or a pharmaceutically acceptable form thereof, or a pharmaceutical composition comprising ziftomenib or a pharmaceutically acceptable form thereof.

[0011] Also provided herein is a pharmaceutical composition comprising an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or a sub-maximum tolerated dose of ziftomenib or a pharmaceutically acceptable form thereof. In some embodiments, the optimal biological dose, the recommended Phase 2 dose, the safe and effective dose, or the sub-maximum tolerated dose is 600 mg. In some embodiments, the ziftomenib or a pharmaceutically acceptable form thereof has a breakthrough therapy designation.

INCORPORATION BY REFERENCE

[0012] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

[0013] FIG. 1: Trough concentrations of ziftomenib in plasma (ng/mL) or in bone marrow, heart, or spleen tissue (ng/g) after daily dosing.

[0014] FIG. 2 : Mean change from baseline of peripheral blasts (orange) and white blood cells (blue) at (a) Cycle 1, Day 8; (b) Cycle 1, Day 15; and (c) Cycle 2, Day 1.

[0015] FIGS. 3A-C: Exposure levels as determined by AUC _0-24 , C _trough , and C _max at steady state following daily ziftomenib dosing at 50, 200, 400, 600, and 800 mg. FIG. 3A: AUC0-24 at steady state. FIG. 3B: C _trough levels at steady state. FIG. 3C: C _max levels at steady state.

[0016] FIGS. 4A-4B: MEIS1 expression by genetic subtype as a function of dose. FIG. 4A: Individual subject data. FIG. 4B: Mean expression levels.

DETAILED DESCRIPTION

[0017] Epigenetic modifications in the lysine methyltransferase 2A (KMT2A) gene result in KMT2A fusions with more than 60 partner genes and play a causative role in the onset, development, and progression of a subset of acute leukemias (Borkin et al., Cancer Cell 2015, 27(4), 589-602.) H0XA9 and MEIS1 are key oncogenes overexpressed in KMT2A -rearranged leukemias. (Thiel et al., Bioessays 2012, 34(9), 771-780.) The H0XA9 andMEIS1 transcription factors drive AML by upregulating stem cell programs and blocking myeloid differentiation. KMT2A(MLL) rearrangements alter normal histone methyltransferase function of KMT2A(MLL) and deregulate these HOX genes, resulting in sustained high HOX levels and blockage of hematopoietic (myeloid) differentiation, ultimately leading to acute leukemia. (Kiihn et al., Cancer Discov. 2016, 6(10), 1166-1181; Klossowski et al., J. Clin. Invest. 2020, 130(2), 981-997; Issa et al., Blood Cancer J. 2021, 11(9), 162; Chan et al., Front. Cell Dev. Biol. 2019, 7, 81.) Translocations (rearrangements) in the KMT2A gene (KMT2AX) occur in 5-10% of AML patients, and the 5-year survival rate of KMT2A-r patients is less than 20% (Issa, 2021). [0018] Nucleoplasmin 1 (NPMP) encodes for a protein involved in cellular protein transport to the nucleolus. NPM1 is also dependent on the interaction between menin and wild-type KMT2A(MLL) to drive leukemogenic gene expression. (Kiihn, 2016.) The NPM1 gene is up- regulated, mutated, and chromosomally translocated in many tumor types.

[0019] In AML, a key common factor in the regulation of these leukemogenic genes by KMT2A(MLL) is the interaction between the KMT2A(MLL) N-terminal portion and menin, which is essential for the vectoring of the gene activating effect of both wild-type KMT2A(MLL) and KMT2A(MLL) fusion proteins to H0XA9 and MEIS1 promoter regions. Menin is a highly specific and direct binding partner of KMT2A(MLL) and KMT2A(MLL) fusion proteins that is required for regulation of their target genes (Yokoyama et al., Cell 2005, 123(2), 207-218.) Numerous studies have demonstrated a critical role of menin as an oncogenic cofactor in leukemic transformation mediated by KMT2A(MLL) fusion proteins and, more recently, menin has also been shown to drive overexpression of H0XA9 and MEIS i1n a subset of normal karyotype AMLs associated with NPM1 mutations. (Yokoyama 2005; Caslini et al., Cancer Res. 2007, 67(15), 7275-7283; Yokoyama et al., Cancer Cell 2008, 14(1), 36-46.; Kühn, 2016.) NPM1 mutations occur in 25-30% of AML patients with or without other mutations and the 5-year survival rate for AML patients with NPM1 mutations (NPM1-m) is about 50% (Angenendt et al., J. Clin. Oncol. 2019, 37(29), 2632-2642; Thiede et al., Blood 2006, 107(10), 4011-4020).

[0020] Additional genetic modifications that negatively impact disease progression and prognosis include mutations to another histone methyltransferase gene, called SET domain containing 2 (SETD2), including truncating mutations, which are found in 1-2% of AML cases, and the gene that encodes for runt-related transcription factor 1, also known as acute myeloid leukemia 1 protein (RUNX1), which is a transcription factor that regulates the differentiation of hematopoietic stem cells into mature blood cells. Chromosomal translocations involving RUNX1 are associated with several types of leukemia including AML.

[0021] Standard of care treatment for AML and ALL is intensive chemotherapy (combination of an anthracycline, such as daunorubicin or idarubicin, and cytarabine, in a “7+3” regimen), which has been in use for more than 40 years. However, intensive chemotherapy has a range of challenging side effects and is not appropriate for patients (such as the elderly) in poor health, and outcomes with standard chemotherapy remain unsatisfactory. In addition, even when patients respond, more than half of adult patients and around 80% of elder patients develop into primary refractoriness, relapse, or treatment-related mortality. Although improvements in supportive care have improved overall survival (OS), up to 30-40% of patients will have refractory disease (i.e., failure to achieve a morphological complete response (CR) after one to two cycles of induction therapy), and these patients have a median survival of less than one year. (Horibata et al., Proc. Natl. Acad. Sci. 2019, 116(21), 10494-10503.) Patients may also be treated through stem cell transplants.

[0022] AML comprises approximately 30% of all adult leukemia cases and 80% of all acute leukemia cases in adults. Outcomes for patients with AML are often considered dire or poor, where outcomes are further characterized by high mortality rates. In particular, the presence of an NPM1-m is correlated with refractory risk to standard intensive induction therapy, as more than 50% of patients who achieve a complete response to induction therapy will relapse within one to three years, while KMT2A-r result in an aggressive and poor prognostic group of blood cancers. (Horibata, 2019; Wang et al., Blood 2020, 136(Suppl. 1), 7.) There remains a need for new therapeutic treatments for NPM1-m and KMT2A-r AML.

[0023] Ziftomenib (KO-539) is potent and selective inhibitor of the menin-KMT2A(MLL) complex that has downstream effects on H0XA9/MEIS1 expression. (Burrows et al., Proceedings of the AACR EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol. Cancer Ther. 2018;17(l Suppl): Abstract nr LB-A27.) KOMET-001 (NCT04067336) is a Phase 1/2 open-label study evaluating ziftomenib in adult patients with relapsed and/or refractory AML, including select NPM1 mutations or KMT2A rearrangements, both of which represent subtypes of this particularly aggressive form of blood cancer for which there is a high unmet need, particularly once the disease has relapsed or become refractory to available therapies. (See https://kuraoncology.com/clinical- trials/clinical-trials-komet-001/, accessed October 2023.) In this study, the safety and tolerability, pharmacokinetics, and anti-tumor activity of ziftomenib in these AML groups is investigated. Endpoints of the study also included determination of an optimal biological dose or recommended Phase 2 dose.

[0024] Provided herein are methods of treating acute leukemia, such as AML or ALL, in particular AML, wherein the methods in some aspects comprise administering ziftomenib to the individual at a daily dose of 600 mg. The methods provided herein generally encompass the finding that individuals having acute leukemia, e.g., AML or ALL, in particular AML, wherein the acute leukemia is menin-dependent, or wherein the acute leukemia comprises a mutation in the NPM1 gene, a rearrangement in the KMT2A gene, a mutation in the SETD2 gene, or a mutation in the RUNX1 gene, or comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-VVD mutation, a SETD2 mutation, aRUNX1 mutation, aFLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, in particular comprising a mutation in AXQ NPMI gene, demonstrate increased response rates and/or improved safety profiles when treated with ziftomenib. For example, treatment of NPM1-m AML comprising administering 600 mg of the menin inhibitor ziftomenib was more efficacious than treatment of non-NPM1-m AML at the same dose and produced a more favorable safety profile. Accordingly, in some embodiments, provided herein are methods of treating AML in an individual, wherein the AML comprises an NPM1 mutation, comprising administering 600 mg of ziftomenib or a pharmaceutically acceptable form thereof to the individual. In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3- ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0025] Furthermore, in some embodiments, provided are uses of ziftomenib or a pharmaceutically acceptable form thereof in a method of treating acute leukemia (e.g., AML or ALL, in particular AML) in an individual, wherein the acute leukemia is menin-dependent, or wherein the acute leukemia comprises an NPM1 mutation, a rearrangement in the KMT2A gene, a mutation in the SETD2 gene, or a mutation in the RUNX1 gene, or wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, in particular a mutation in the NPM1 gene. Also provided are uses of ziftomenib or a pharmaceutically acceptable form thereof in a method of treating AML with an NPM1 mutation. Similarly, in some embodiments, provided is ziftomenib or a pharmaceutically acceptable form thereof for use in treating acute leukemia (e.g., AML or ALL, in particular, AML) in an individual, wherein the AML comprises an NPM1 mutation, a rearrangement in the KMT2A gene, a mutation in the SETD2 gene, or a mutation in the RUNX1 gene, in particular a mutation in the NPM1 gene. In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

Ziftomenib and Pharmaceutically Acceptable Forms

[0026] Ziftomenib is a potent (IC5022 nM) and selective inhibitor of the menin-MLL(KMT2A) interaction in clinical development for treatment of acute leukemias, including NMP1 -mutated (NPM1-m) and KMT2A -rearranged (KMT2A-r) AML, and other genetically defined acute leukemia subgroups with high unmet need.

[0027] Ziftomenib is a compound having the structure:

(ziftomenib), alternatively named as (5)-4-methyl-5-((4-((2-(methylamino)-6-(2,2,2-trifluoroethyl )thieno[2,3- d]pyrimidin-4-yl)amino)piperidin- 1 -yl)methyl)- 1 -(2-(4-(methylsulfonyl)piperazin- 1 -yl)propyl)- 1H -indole-2-carbonitrile. In some embodiments, the methods described herein employ a pharmaceutically acceptable form of ziftomenib. In some embodiments, the methods described herein employ ziftomenib or a pharmaceutically acceptable salt thereof. In some embodiments, the methods described herein employ ziftomenib or a solvate thereof. In certain embodiments, ziftomenib comprises the free base form or a solvate thereof. Also included, in some embodiments, are stereoisomers and/or metabolites of ziftomenib. [0028] In some embodiments, the menin inhibitor described herein is ziftomenib or a pharmaceutically acceptable form thereof.

Doses and Dosing Regimens of Ziftomenib

[0029] In some embodiments, the methods provided herein comprise administering an effective amount, such as 600 mg, of ziftomenib or a pharmaceutically acceptable form thereof daily to an individual. In some embodiments, the methods comprise administering an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or a dose below the maximum tolerated dose of ziftomenib or a pharmaceutically acceptable form thereof daily to an individual. In some embodiments, the optimal biological dose is 600 mg. In some embodiments, the recommended Phase 2 dose (RP2D) is 600 mg. In some embodiments, the safe and effective dose is 600 mg. In some embodiments, the dose below the maximum tolerated dose is 600 mg. In some embodiments, the 600 mg dose is a safe and effective amount. In some embodiments, the ziftomenib or a pharmaceutically acceptable form thereof has a breakthrough therapy designation. [0030] In some embodiments, the administering of ziftomenib or the pharmaceutically acceptable form thereof comprises administering to the individual for at least 3 days, or for at least 5 days, or for at least 7 days, or for at least 10 days, or for at least 14 days, or for at least 21 days, or for at least 28 days, or for a cycle comprising at least 28 days, or for a cycle comprising 28 days.

[0031] In certain embodiments, ziftomenib or a pharmaceutically acceptable form thereof is administered daily to the individual for a cycle comprising at least 28 days, or comprising 28 days, for N cycles, wherein N is at least 1. In certain embodiments, N is at least 2. In certain embodiments, N is at least 3. In certain embodiments, N is at least 4. In certain embodiments, N is 2. In certain embodiments, N is 3. In certain embodiments, N is 4. In certain embodiments, N is 5. In certain embodiments, N is 6. In certain embodiments, N is 7. In certain embodiments the cycles are continuous (i.e., 0 days between cycles).

[0032] In certain embodiments, ziftomenib or a pharmaceutically acceptable form thereof is administered orally.

[0033] In some embodiments, administering daily is administering once or twice daily. In some embodiments, administering daily is once daily.

[0034] Dose amounts of ziftomenib as presented herein refer to the free base amount (if using the free form) or to the free base equivalent amount (if using a salt and/or solvate). Thus, for example, if a salt form were used, the total mass amount for the daily dose would exceed 600 mg, but the total mass amount would be selected to provide 600 mg ziftomenib free base equivalent.

[0035] In some embodiments, ziftomenib or a pharmaceutically acceptable form thereof is administered in combination with a P-gp inhibitor or breast cancer resistance protein (BCRP) inhibitor.

Pharmaceutical Compositions

[0036] Also provided herein is a pharmaceutical composition comprising an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or a sub-maximum tolerated dose of ziftomenib or a pharmaceutically acceptable form thereof. In some embodiments, the optimal biological dose, the recommended Phase 2 dose, the safe and effective dose, or the sub-maximum tolerated dose is 600 mg. In some embodiments, the ziftomenib or a pharmaceutically acceptable form thereof has a breakthrough therapy designation. In some embodiments, the pharmaceutical composition comprises one or more dosage forms, such as one or more oral dosage forms, optionally wherein each oral dosage form comprises from 50 to 600 mg of ziftomenib, or comprises 50 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg, or 600 mg of ziftomenib. In some embodiments, the total ziftomenib in the one or more oral dosage forms is 600 mg. In some embodiments, each oral dosage form comprises 100 mg, 200 mg, or 300 mg of ziftomenib. In some embodiments, each oral dosage form comprises 200 mg or 300 mg of ziftomenib. In some embodiments, the ziftomenib administered in the methods provided herein is administered using such pharmaceutical composition or oral dosage form(s).

AML and ALL

[0037] In some embodiments, the methods provided herein are directed to treating acute myeloid leukemia (AML). AML is a disease of the bone marrow and a disorder of hematopoietic stem cells characterized by genetic alterations in blood-cell precursors resulting in overproduction of neoplastic clonal myeloid stem cells. While extramedullary manifestations can occur (e.g., myeloid sarcomas, leukemia cutis), the underlying disease is generally due to abnormalities in hematologic cellular production. In certain embodiments, the acute myeloid leukemia (AML) comprises relapsed AML, refractory AML, or both relapsed and refractory AML. In certain embodiments, AML is refractory AML. In certain embodiments, refractory disease is refractory to intensive chemotherapy (first line standard of care), including cytarabine and an anthracycline (idarubicin or daunorubicin), typically as a 7+3 combination of a continuous infusion of cytarabine and intermittent dosing of the anthracycline administered over 7 days and 3 days, respectively. In certain embodiments, the first line standard of care for newly diagnosed AML in patients ineligible or unit for the 7+3 regimen is venetoclax plus azacitadine (ven/aza). In some embodiments, the AML is resistant to ven or ven/aza. In some embodiments, the AML has progressed on or after treatment with ven or ven/aza. In some embodiments, the AML is relapsed AML. In some embodiments, the AML is both refractory and relapsed AML. In some embodiments, the AML is acute promyelocytic leukemia, acute myeloblastic leukemia, or acute megakaryoblastic leukemia.

[0038] In some embodiments, the methods provided herein are directed to treating acute lymphocytic leukemia (ALL). ALL is a type of cancer of the blood and bone marrow involving uncontrolled proliferation of abnormal, immature lymphocytes, leading to the replacement of bone marrow and invasion of the blood. In certain embodiments, the ALL comprises relapsed ALL, refractory ALL, or both relapsed and refractory ALL. In certain embodiments, ALL is refractory ALL. In some embodiments, the ALL is relapsed ALL. In some embodiments, the ALL is both refractory and relapsed ALL. In some embodiments, the ALL is precursor B acute lymphoblastic leukemia, precursor T acute lymphoblastic leukemia, Burkitt's leukemia, or acute biphenotypic leukemia.

Genetic Alterations in Acute Leukemias

[0039] In some embodiments, the acute leukemia or leukemia cell is characterized by a (e.g., one or more) genetic alteration, which can be selected from an NPM1 mutation, a KMT2A rearrangement, an SETD2 mutation, and a RUNX1 mutation. In some embodiments, the acute leukemia or leukemia cell is menin dependent. In some embodiments, the acute leukemia or leukemia cell comprises an NPM1 mutation. In some embodiments, the acute leukemia or leukemia cell comprises a KMT2A rearrangement. In some embodiments, the acute leukemia or leukemia cell comprises a KMT2A-PT . In some embodiments, the acute leukemia or leukemia cell comprises an SETD2 mutation. In some embodiments, the acute leukemia or leukemia cell comprises a RUNX1 mutation. In some embodiments, the acute leukemia or leukemia cell comprises an SETD2 mutation and aRUNX1 mutation. In some embodiments, the acute leukemia or leukemia cell comprises one or more mutations selected from FLT3, FLT3-ITD, FLT3-TKD, IDH, IDH I, IDH 2, TERT, and BRAF. In some embodiments, the acute leukemia or leukemia cell comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3-ITD mutation, a FLT3-TKD mutation, an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof. In some embodiments, the acute leukemia or leukemia cell comprises an NPM1 mutation and optionally comprises one or more mutations selected from FLT3 (such as FLT3-ITD or FLT3-TKD), IDH (such as an IDH1 mutation or an IDH2 mutation), TERT, or BRAF. In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-internal tandem duplication (ITD) mutation or a FLT3 mutation in the tyrosine kinase domain (FLT3-TKD mutation)) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0040] In certain embodiments, a mutated NPM1 gene comprises one or more mutations relative to the wildtype NPM1 gene sequence. NPM1 generally refers to and encompasses the gene encoding the NPM1 protein (e.g., see UniProt ID P06748). In certain instances, the NPM1 gene encompasses NCBI Gene ID 4869 and/or NCBI Reference Sequence: NG 016018.1 (5001..28181). NPM1 mutations are found in about 25-30% of AML cases, and in certain instances, are generally characterized by the presence a canonical 4-base pair insertion that generates a new N-terminal nuclear export signal, leading to aberrant cytoplasmic accumulation of the mutant NPMlc protein. NPM1 mutations include Type A, B, and D mutations characterized by a 4-nucleotide insertion in exon 12 that results in cytoplasmic localization of NPM1 (NPM1- c). In certain instances, NPMl-c binds to and, consequently, mislocalizes transcription factors, which normally promote myeloid lineage differentiation but may also be re-imported into the nucleus by XPO1 and directly affect gene expression.

[0041] In certain embodiments, the NPM1 mutation comprises a Type A, Type B, Type C, or Type D mutation. In certain embodiments, the NPM1 mutation comprises a Type A mutation. In certain embodiments, the NPM1 mutation comprises a Type B mutation. In certain embodiments, NPM1 mutation comprises a Type C mutation. In certain embodiments, NPM1 mutation comprises a Type D mutation. In certain embodiments, NPM1 mutation results in cytoplasmic localization of NPM1. In certain embodiments, the NPM1 mutation comprises an insertion (e.g., a 4-nucleotide insertion) in exon 12 of an NPM1 gene.

[0042] Multiple translocations involving the KMT2A gene have been reported in both AML and ALL. The KMT2A-MLLT3 fusion caused by t(9; 11)(p21.3;q23.3) is the most common KMT2A rearrangement in adults with AML, but more than 80 different fusion partners have been described. The translocation (9;l l)(p22;q23) (MLLT3; KMT2A) or t(10;l I)(pl2;q23) (AF10; KMT2A) have been reported in 4% of adult myeloid leukemias. Similarly, multiple SETD2 mutations and RUNX1 mutations that are implicated in acute leukemias have been reported.

[0043] In some embodiments, the acute leukemia or leukemia cell comprises more than one mutation or rearrangement. In some embodiments, the acute leukemia or leukemia cell comprises (a) an NPM1 mutation or a KMT2A rearrangement, and (b) at least one mutation selected from FLT3 (such as FLT3-ITD or FLT3-TKD), IDH (such as IDH1 or IDH2) TERT, and BRAF. In some embodiments, the acute leukemia or leukemia cell comprises (a) an NPM1 mutation and (b) at least one mutation selected from a FLT3 mutation (such as FLT3-ITD or FLT3-TKD), or IDH (such as IDH1 or IDH 2).

[0044] In certain instances, characterization of a genetic mutation or rearrangement can be achieved via collection of bone marrow (BM aspirate), a whole blood sample, and/or tumor sample followed by known assays for the analysis of nucleic acids. In certain embodiments, a mutation or rearrangement is detected by sequencing (e.g., genomic sequencing), such as by My AML®, a CLIA-vali dated, next-generation sequencing assay mutations in 194 genes associated with AML. In certain embodiments, a particular mutation or rearrangement is detected by molecular testing, such as by polymerase chain reaction (e.g., followed by fragment analysis and/or capillary gel electrophoresis). In certain embodiments, a mutation or rearrangement is detected by RT-PCR or quantitative PCR. In some embodiments, the methods provided herein comprise detecting a mutation or rearrangement or receiving an identification of the mutation or rearrangement prior to administering ziftomenib, in particular an NPM1 mutation, optionally wherein the NPM1 mutation is detected by a next-generation sequencing assay or a PCR assay.

Efficacy

[0045] As described in Example 3, efficacy outcomes for patients treated with ziftomenib were evaluated according to rates of CR, CR/CRh, and CRc, and by ORR. In some embodiments, the CR or CR/CRh rate is at least about 18%, or at least about 19%, or at least about 20%, or at least about 21%, or at least about 22%, or at least about 23%, or at least about 24%, or at least about 25%, or at least about 26%, or at least about 27%, or at least about 28%, or at least about 29%, or at least about 30%, or at least about 31%, or at least about 32%, or at least about 33%, or at least about 34%, or at least about 35%, or is about 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, or 35%, or is about 35%. In some embodiments, the CR rate is at least about 35%, or is about 35%. In some embodiments, the CRc rate is at least about 20%, or at least about 21%, or at least about 22%, or at least about 23%, or at least about 24%, or at least about 25%, or at least about 26%, or at least about 27%, or at least about 28%, or at least about 29%, or at least about 30%, or at least about 31%, or at least about 32%, or at least about 33%, or at least about 34%, or at least about 35%, or at least about 36%, or at least about 37%, or at least about 38%, or at least about 39%, or at least about 40%, or is about 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, or 40%. In some embodiments, the ORR is at least about 20%, or at least about 21%, or at least about 22%, or at least about 23%, or at least about 24%, or at least about 25%, or at least about 26%, or at least about 27%, or at least about 28%, or at least about 29%, or at least about 30%, or at least about 31%, or at least about 32%, or at least about 33%, or at least about 34%, or at least about 35%, or at least about 36%, or at least about 37%, or at least about 38%, or at least about 39%, or at least about 40%, or at least about 41%, or at least about 42%, or at least about 43%, or at least about 44%, or at least about 45%, or is about 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, or 45%.

[0046] In some embodiments, the CR, CR/CRh, CRc, and/or ORR rates are higher for patients with particular genetic characteristics. In some embodiments, the CR, CR/CRh, CRc, and/or ORR rates are higher for patients with acute leukemia (such as AML) with an NPM1 mutation than for patients without an NPM1 mutation.

[0047] In some embodiments, the duration of remission (DoR) for patients, such as NPMl-m AML patients, who achieve CRc is at least 2 months, or at least 3 months, or at least 4 months, or at least 5 months, or at least 6 months, or at least 7 months, or at least 8 months, or at least 9 months, or at least 10 months, or at least 11 months, or at least 12 months, or at least about 18 months, or at least about 24 months. In some embodiments, the DoR for NPMl-m patients that achieve CRc is at least about 8 months, or at least about 8.2 months, or is about 8.2 months. In some embodiments, the DoR for NPMl-m patients who achieve CRc is at least about 5 months, or at least about 6 months, or at least about 7 months, or is about 5.6 months, or is about 6.6 months, or is about 7.7 months. In some embodiments, the DoR for NPMl-m patients who achieve CRc from administration of 600 mg ziftomenib is about 5 to 7 months, or about 5.6 months, or about 6.6 months. In some embodiments, the DoR for NPMl-m patients who achieve CR or CRh is about 5 to 7 months, or about 5.6 months, or about 6.6 months. In some embodiments, the DoR for NPMl-m patients who achieve CR or CRh from administration of 600 mg ziftomenib is 5 to 6 months, or about 5.6 months. In some embodiments, the DoR for NPM1- m patients treated according to the methods described herein is longer than the DoR for KMT2A- r patients.

[0048] In some embodiments, median overall survival (OS) is at least about 5 months, or is about 5.1 months, or is about 5.6 months, or is at least 5 months, or is at least 5.5 months. In some embodiments, such OS is achieved by NPMl-m patients treated with 600 mg ziftomenib. In some embodiments, the OS for NPMl-m patients treated with 600 mg ziftomenib is longer than for NPMl-m patients treated with 200 mg ziftomenib.

[0049] In some embodiments, the administering produces a transient increase in white blood cell count or in peripheral blast count, followed by a reduction in such a count. In some embodiments, the transient increase occurs within 14 days of initiation of treatment. In some embodiments, the reduction occurs within 14 days of the increase. In some embodiments, provided herein are methods of transiently increasing white blood cell counts or peripheral blast counts comprising administering an effective amount of ziftomenib or a pharmaceutically acceptable form thereof, for example 600 mg ziftomenib or a pharmaceutically acceptable form thereof. In some embodiments, the increase from baseline occurs within one week, two weeks, three weeks, or four weeks, from initiation of the administering. In some embodiments, the increase from baseline lasts for about one week, about two weeks, or about three weeks.

Safety

[0050] In some embodiments, the methods provided herein comprise administering ziftomenib or a pharmaceutically acceptable form thereof to the individual, wherein the risk of the individual of one genetic subtype exhibiting or developing a particular side effect (or a severe side effect) is reduced relative another genetic subtype or the overall treated patient population. As used herein, the “risk” of an individual exhibiting or developing a particular side effect is determined based on the incidence rate for the side effect across the modified intent-to-treat (mITT) patient population regardless of dose, as the results demonstrated that safety outcomes did not correlate completely with dose (see Example 3), or based on the incidence rate for the side effect across different genetic cohorts (e.g., NPMl-m compared to KMT2A-r groups).

[0051] In some embodiments, the methods disclosed herein include the feature that the risk of the individual developing certain adverse events is lower where individual has an acute leukemia with nNPM1 mutation (e.g., AML or ALL), in particular AML, than for an individual not having an NPM1 mutation. In some embodiments, the risk of developing a Grade 3 or higher (i.e., Grade 3, 4, or 5) treatment-emergent adverse event (TEAE) regardless of causality, a serious adverse event regardless of causality, a differentiation syndrome-suspect adverse event, differentiation syndrome, or severe differentiation syndrome, is lower for an individual with acute leukemia that comprises an NPM1 mutation than for an individual with acute leukemia that does not comprise an NPM1 mutation.

[0052] In some embodiments, the methods comprise administering ziftomenib or a pharmaceutically acceptable form thereof, wherein a risk of the individual to whom ziftomenib is administered of developing any Grade 3 or higher treatment-emergent adverse event (TEAE) regardless of causality after the administering is less than about 80%, or less than about 75%, or is about 71%. In some embodiments, the methods comprise administering ziftomenib or a pharmaceutically acceptable form thereof, wherein a risk of the individual developing any serious adverse event regardless of causality after the administering is less than about 65%, or less than about 60%, or less than about 55%, or is about 53%.

[0053] In some embodiments, the methods comprise administering ziftomenib or a pharmaceutically acceptable form thereof, wherein a risk of the individual developing any differentiation syndrome-suspect adverse event after the administering is less than about 80%, or less than about 75%, or less than about 70%, or less than about 65%, or less than about 60%, or less than about 55%, or less than about 50%, or is about 47%. As used herein, a “differentiation syndrome-suspect adverse event” is differentiation syndrome, a treatment-emergent adverse event (TEAE) meeting the Norsworthy Criteria for possible differentiation syndrome, or a TEAE meeting the Norsworthy Criteria where differentiation syndrome cannot be excluded. (Norsworthy et al., Clin. Cancer Res. 2020, 26(16), 4280-4288.)

[0054] In some embodiments, the methods comprise administering ziftomenib or a pharmaceutically acceptable form thereof, wherein a risk of the individual developing differentiation syndrome after the administering is less than about 25%, or less than about 20%, or less than about 19%, or less than about 18%, or is about 18%. In some embodiments, the probability of the differentiation syndrome the individual has developed will be severe differentiation syndrome of Grade 3, 4, or 5, is less than about 50%, or less than about 45%, or less than about 40%, or less than about 35%, or is about 33%. [0055] In some embodiments, the methods comprise administering ziftomenib or a pharmaceutically acceptable form thereof, wherein the risk of the individual developing severe differentiation syndrome is less than about 20%, or less than about 15%, or less than about 10%, or less than about 7%, or is about 6%. As used herein, “severe differentiation syndrome” is defined as differentiation syndrome at Grade 3, Grade 4, or Grade 5 on the National Cancer Institute’s standardized Common Toxicity Criteria for Adverse Events (found at http://ctep.cancer.gov/protocolDevelopment/electronic_applic ations/ctc.htm).

[0056] In some embodiments, the methods comprise administering ziftomenib or a pharmaceutically acceptable form thereof, wherein an individual develops differentiation syndrome after the administering, and the probability that the differentiation syndrome is not severe differentiation syndrome (e.g., is Grade 1 or 2) is greater than about 50%, or greater than about 55%, or greater than about 60%, or greater than about 65%, or is about 67%.

[0057] In some embodiments, the methods provided herein comprise administering ziftomenib or a pharmaceutically acceptable form thereof without inducing QTc prolongation.

Differentiation Disorders

[0058] In preclinical studies, ziftomenib was found to drive terminal differentiation and scheduled apoptosis. One potential serious sequela is differentiation syndrome (DS), which can be life-threatening or fatal if not treated. Differentiation syndrome has been noted in patients treated with isocitrate dehydrogenase (IDH) inhibitors (Norsworthy, 2020) and it has been reported in patients following administration of ziftomenib, with some fatal outcomes. Increased recognition of the signs and symptoms of DS through the framework of Montesinos can lead to earlier diagnosis and treatment and reduced rates of severe complications and mortality. Montesinos et al. (Blood 2009, 113(4), 775-783) proposed diagnostic criteria for DS based on at least two of the following signs and symptoms: dyspnea, unexplained fever, weight gain, unexplained hypotension, acute kidney injury, and pulmonary infiltrates or pleuropericardial effusion. Patients with two or three criteria are classified as having moderate DS and patients with at least four criteria were classified as having severe DS.

[0059] As used herein, “differentiation disorder” refers to differentiation syndrome (with or without hyperleukocytosis), hyperleukocytosis, and tumor lysis syndrome. Hyperleukocytosis can be detected based on increasing white blood cell counts in the absence of an infection. Tumor lysis syndrome can occur in settings of rapidly progressive leukocytosis and can be detected by the presence of two or more of blood chemistry markers selected from hyperuricemia, hyperkalemia, hyperphosphatemia, and hypocalcemia, or by an increased serum creatinine level. [0060] Using the algorithm based on Montesinos criteria, as described by Norsworthy (2020), the following adverse events were monitored and evaluated for treated patients, and diagnostic criteria applied as described below in those patients who received at least one dose of ziftomenib. [0061] A differentiation disorder, such as DS, with or without hyperleukocytosis, may be suspected based on one or more of the following symptoms:

• New or worsening progressive dyspnea or hypoxia, with increasing demands for supplemental oxygen and without a clear alternative etiology

• Radiologic evidence of new or worsened pulmonary infiltration, not attributable to another cause;

• Radiologic evidence of new or worsened pleural or pericardial effusion that has no definitive etiology or is refractory to treatment for the initially suspected cause;

• New or worsened peripheral edema without definitive etiology, with rapid weight gain (e.g., > 5 kg over 7 days);

• Acute renal failure (e.g., increase in serum creatinine > 2-fold from baseline) not attributable to other cause or medication;

• Unexplained fever > 38° C (100.4° F);

• Unexplained hypotension;

• Significant changes in markers of inflammation;

• Evidence of multiorgan dysfunction; or

• Rash, joint pain, bone pain, or swelling of extramedullary lesions.

[0062] The presence of two or more of the above signs and symptoms may be considered potential DS. Patients with two or three criteria are classified as having moderate DS, and those with at least 4 criteria are classified as having severe DS.

[0063] Notably, development of differentiation syndrome in patients with AML with an NPM1 mutation was found to correlate with favorable outcomes. In some embodiments, the treated individual develops differentiation syndrome, optionally wherein the differentiation syndrome is severe differentiation syndrome (e.g., Grade 3, 4, or 5), yet has a probability of achieving ORR of at least about 60%, or at least about 65%, or at least about 70%, or at least about 75%, or of about 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, or 75%. [0064] It was also discovered that treatment of patients with ziftomenib or a pharmaceutically acceptable form thereof increased the level of myeloid blasts in the blood of treated individuals. Thus, provided herein are methods of increasing the level of myeloid blasts in the blood of an individual with AML comprising administering an effective amount of a menin inhibitor, in particular 600 mg of ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual, optionally wherein the AML is menin-dependent, or optionally wherein the AML comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A-PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or optionally wherein the AML comprises an NPM1 mutation, a KMT2A rearrangement, an SETD2 mutation, or a RUNX1 mutation. In some embodiments, the AML comprises an NPM1 mutation or a KMT2A rearrangement. In some embodiments, the AML comprises an NPM1 mutation. In some embodiments, the relative levels of myeloid blasts in the blood of the individual that has been assessed by analysis of two time- separated blood samples from the individual, optionally wherein the blood samples are taken at, for example, (a) a first timepoint and a second timepoint, wherein both timepoints are during the administering or (b) at a first timepoint prior to beginning the administering and at a second timepoint during the administering. In some embodiments, the first timepoint is prior to the administering, e.g., prior to Cycle 1, Day 1, and the second timepoint is at least 7, 14, 21, or 28 days later, or is a day from Cycle 1, Day 2, to Cycle 1, Day 28. In some embodiments, each analysis is a complete blood count (CBC), optionally with differential. In some embodiments, the first timepoint and the second timepoint are separated by one day, two days, three days, four days, five days, six days, one week, two weeks, three weeks, four weeks, at least one week, at least two weeks, at least three weeks, or at least four weeks, or by the duration of one cycle (such as Cycle 1), or wherein the second timepoint is at the time when the individual reaches a complete remission (CR). In some embodiments, the first timepoint is at screening, or is on Cycle 1, Day 1. In some embodiments, the increase in the level of myeloid blasts in the blood of the individual is not correlated with progression of the AML. In some embodiments, the increase in the level of myeloid blasts occurs in the extramedullary space. In some embodiments, the increase in the level of myeloid blasts indicates the individual is sensitive to the menin inhibitor, in particular ziftomenib or a pharmaceutical form thereof. Monitoring and Treatment of Differentiation Disorders

[0065] It was discovered that monitoring and early intervention can reduce the incidence and severity of differentiation disorders, allowing for fewer adverse events and enabling patients to remain on treatment.

[0066] In some embodiments, the methods provided herein comprise administering an effective amount of a steroid (e.g., dexamethasone) if a differentiation disorder is detected in the individual during the administering of the ziftomenib or the pharmaceutically acceptable form thereof.

[0067] Provided herein are methods of identifying an acute leukemia (in particular AML) in an individual as sensitive to administration of a menin inhibitor, in particular ziftomenib, comprising: administering an effective amount of the menin inhibitor, in particular 600 mg ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual, receiving an identification of the level of myeloid blasts in a first blood sample taken from the individual at a first timepoint that is either before initiation of the administering or during the administering, receiving an identification of the level of myeloid blasts in a second blood sample taken from the individual at a second timepoint that is after the first timepoint and that is during the administering, and determining that the acute leukemia is sensitive to the administering if the level of myeloid blasts at the second timepoint is greater than the level at the first timepoint, optionally wherein the acute leukemia is menin-dependent, or optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A -PTD mutation, a SETD2 mutation, a RUNX1 mutation, a FLT3 mutation (such as a FLT3ATD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNXl mutation, preferably an NPM1 mutation or a KMT2A rearrangement.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with a FLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0068] In some embodiments are methods of treating a differentiation disorder, in particular tumor lysis syndrome, in an individual diagnosed with the differentiation disorder in an individual with acute leukemia, or reducing the risk of developing a severe differentiation disorder in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent, or optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a KMT2A -PTD mutation, aSETD2 mutation, aRUNXl mutation, a.FLT3 mutation (such as a FLT3- ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably an NPM1 mutation or a KMT2A rearrangement, comprising:

(a) administering an effective amount of a menin inhibitor, in particular 600 mg of ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual,

(b) administering IV hydration to the individual, and optionally,

(c) administering an effective amount of a xanthine oxidase inhibitor to the individual, optionally wherein the xanthine oxidase inhibitor is allopurinol, optionally administering the allopurinol at a dose of about 200-400 mg/m ² /day in 1-3 divided doses, up to a maximum of about 800 mg daily.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with aFLT3 mutation (such as a FLT3-internal tandem duplication (ITD) mutation or aFLT3 mutation in the tyrosine kinase domain (FLT3-TKD mutation)) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0069] Some embodiments comprise administering the xanthine oxidase inhibitor, and comprising, prior to administering the xanthine oxidase inhibitor, diagnosing the individual as having a low or intermediate risk of having or developing the differentiation disorder from receiving an identification that the individual has:

(1) a white blood count of less than about 25 x 10 ⁹ L and a lactate dehydrogenase level of less than twice the upper limit of normal (e.g., where a normal level is about 280 units/L), or

(2) a white blood count from about 25 to about 100 x 10 ⁹ /L, or

(3) a white blood count of less than about 25 x 10 ⁹ /L and a lactate dehydrogenase level that is more than twice the upper limit of normal.

[0070] Provided herein are methods of treating a differentiation disorder in an individual with acute leukemia, or reducing the risk of developing a severe differentiation disorder in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent, or optionally wherein the acute leukemia comprises a mutation selected from an NPM1 mutation, a KMT2A rearrangement, a KMT2A -PTD mutation, aSETD2 mutation, aRUNXl mutation, aFLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably an NPM1 mutation or a KMT2A rearrangement, comprising:

(a) administering an effective amount of a menin inhibitor, in particular 600 mg of ziftomenib or a pharmaceutically acceptable form thereof daily, to the individual,

(b) administering IV hydration to the individual, and

(c) administering a therapeutically effective amount of rasburicase, optionally at a dose of about 0.2 mg/kg, optionally as an intravenous infusion over about 30 minutes daily, for up to about 5 days.

In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with aFLT3 mutation (such as a FLT3-internal tandem duplication (ITD) mutation or aFLT3 mutation in the tyrosine kinase domain (FLT3-TKD mutation)) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0071] Some embodiments comprise, prior to administering the rasburicase, diagnosing the individual as having a high risk of having or developing the differentiation disorder from receiving an identification that the individual has:

(i) has a white blood count level from greater than or equal to about 100 x 10 ⁹ /L, or

(ii) has a white blood count level (i) from about 25 to about 100 x 10 ⁹ /L, or (ii) less than about 25 x 10 ⁹ /L and a lactate dehydrogenase level that is more than twice the upper limit of normal (e.g., where a normal level is about 280 units/L), and, for each of (i) and (ii), wherein the individual has renal dysfunction, or uric acid, potassium, and/or phosphate levels above the applicable upper limit of normal.

[0072] Provided herein are methods of treating a differentiation disorder, or reducing the risk of developing a severe differentiation disorder, in an individual with acute leukemia, optionally wherein the acute leukemia is menin-dependent, or optionally wherein the acute leukemia comprises a mutation selected from an NPM1 mutation, a KMT2A rearrangement, a KMT2A -PTD mutation, a SETD2 mutation, aRUNX1 mutation, aFLT3 mutation (such as a FLT3-ITD mutation or a FLT3-TKD mutation), an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), a TERT mutation, or a BRAF mutation, or any combination thereof, or optionally wherein the acute leukemia comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation, preferably an NPM1 mutation or a KMT2A rearrangement, comprising:

(a) administering a prophylactic and/or effective amount of a corticosteroid to the individual, optionally wherein the corticosteroid is prednisone, optionally at a dose of about 0.5 mg/kg (or an equivalent dose of an alternative corticosteroid); and

(b) administering a therapeutically effective amount of the menin inhibitor to the individual. In some aspects, the acute leukemia comprises an NPM1 mutation, optionally in combination with aFLT3 mutation (such as a FLT3-internal tandem duplication (ITD) mutation or aFLT3 mutation in the tyrosine kinase domain (FLT3-TKD mutation)) or an IDH mutation (such as an IDH1 mutation or an IDH2 mutation), or a combination thereof.

[0073] In some embodiments, wherein the corticosteroid and the menin inhibitor are administered daily, and consecutively or simultaneously, optionally comprising administering the first dose of each of the corticosteroid and the menin inhibitor on or about the same day, or administering the first dose of the corticosteroid on a day that is before or after the first administering of the menin inhibitor.

[0074] In some embodiments, prior to administering the corticosteroid or the menin inhibitor, the individual has one or more of a white blood count of greater than 5 x 10 ⁹ /L, an increased serum creatinine level, significant extramedullary disease, and proliferative acute leukemia.

[0075] In some embodiments, comprising administering the corticosteroid daily starting on a first day, administering the menin inhibitor daily starting on the same or a subsequent day, and reducing the dose of the corticosteroid after administering the menin inhibitor for about 28 days if the individual has not been not diagnosed with the differentiation disorder (in the method of reducing the risk) or if the individual has developed the differentiation disorder and the differentiation disorder improved and bone marrow blasts are at a level of less than about 5% (in the method of reducing the risk or the method of treating).

[0076] Some embodiments comprise administering dexamethasone at a dose of about 5 mg, 10 mg, or 15 mg, preferably 10 mg, or from about 5 to 10 mg, intravenously, every 12 hours (or an equivalent dose of an alternative oral or IV corticosteroid) to the individual, for one, two, or three days.

[0077] Some embodiments comprise administering a therapeutically effective amount of hydroxyurea to the individual if the white blood count or leukocyte count for the individual increases to greater than about 10 x 10 ⁹ /L or doubles within about 24-48 hours, and, optionally, administering a therapeutically effective amount of cytarabine, idarubicin, or gemtuzumab to the individual.

[0078] Some embodiments comprise tapering the dose of and/or discontinuing the administering of the corticosteroid, hydroxyurea, cytarabine, idarubicin, or gemtuzumab upon improvement of the differentiation disorder.

[0079] Some embodiments comprise interrupting the administering of the menin inhibitor during all or part of the administering of one or more of IV hydration, allopurinol, rasburicase, prednisone, dexamethasone, hydroxyurea, cytarabine, idarubicin, and gemtuzumab, and re- initiating the administering after the differentiation disorder improves (for example, when the white blood count drops to less than about 20 x 10 ⁹ /L) at the therapeutically effective dose or a reduced dose of the menin inhibitor.

[0080] In some embodiments, the differentiation disorder is differentiation syndrome with or without hyperleukocytosis. In some embodiments, the differentiation disorder is tumor lysis syndrome.

[0081] In some embodiments, the acute leukemia comprises AML. In some embodiments, the acute leukemia comprises ALL. In some embodiments, the acute leukemia comprises an NPM1 mutation. In some embodiments, the acute leukemia is AML comprising an NPM1 mutation.

Definitions

[0082] Compounds of the present disclosure also include crystalline and amorphous forms of those compounds, pharmaceutically acceptable salts, and active metabolites of these compounds having the same type of activity, including, for example, polymorphs, pseudopolymorphs, solvates, hydrates, unsolvated polymorphs (including anhydrates), conformational polymorphs, and amorphous forms of the compounds, as well as mixtures thereof.

[0083] The compounds described herein may exhibit their natural isotopic abundance, or one or more of the atoms may be artificially enriched in a particular isotope having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number predominantly found in nature. All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are encompassed within the scope of the present disclosure. For example, hydrogen has three naturally occurring isotopes, denoted 1H (protium), 2H (deuterium), and 3H (tritium). Protium is the most abundant isotope of hydrogen in nature. Enriching for deuterium may afford certain therapeutic advantages, such as increased in vivo half-life and/or exposure, or may provide a compound useful for investigating in vivo routes of drug elimination and metabolism. Isotopically-enriched compounds may be prepared by conventional techniques well known to those skilled in the art.

[0084] The term “isotopolog” refers to an isotopically enriched compound. The term “isotopically enriched” refers to an atom having an isotopic composition other than the natural isotopic composition of that atom. “Isotopolog” can also refer to a compound containing at least one atom having an isotopic composition other than the natural isotopic composition of that atom. The term “isotopic composition” refers to the amount of each isotope present for a given atom. Radiolabeled and isotopically enriched compounds are useful as therapeutic agents, e.g., multiple myeloma therapeutic agents, research reagents, e.g., binding assay reagents, and diagnostic agents, e.g., in vivo imaging agents. All isotopic variations of the compounds as described herein, whether radioactive or not, are intended to be encompassed within the scope of the embodiments provided herein.

[0085] “Isomers” are different compounds that have the same molecular formula. “Stereoisomers” are isomers that differ only in the way the atoms are arranged in space. “Enantiomers” are a pair of stereoisomers that are non-superimposable mirror images of each other. A 1 : 1 mixture of a pair of enantiomers is a “racemic” mixture. The term “(±)” is used to designate a racemic mixture where appropriate. “Diastereoisomers” or “diastereomers” include stereoisomers that have at least two asymmetric atoms but are not mirror images of each other. The absolute stereochemistry is specified according to the Cahn-Ingold-Prelog R-S system. When a compound is a pure enantiomer, the stereochemistry at each chiral carbon can be specified by either R or S. Resolved compounds whose absolute configuration is unknown can be designated (+) or (-) depending on the direction (dextro- or levorotatory) in which they rotate plane polarized light at the wavelength of the sodium D line. Certain compounds described herein contain one or more asymmetric centers and can thus give rise to enantiomers, diastereomers, and other stereoisomeric forms, the asymmetric centers of which can be defined, in terms of absolute stereochemistry, as (R)- or (S)-. The present chemical entities, pharmaceutical compositions and methods are meant to include all such possible stereoisomers, including racemic mixtures, optically pure forms, mixtures of diastereomers and intermediate mixtures. Optically active (R)- and (S)-isomers can be prepared using chiral synthons or chiral reagents or can be resolved using conventional techniques. The optical activity of a compound can be analyzed via any suitable method, including but not limited to chiral chromatography and polarimetry, and the degree of predominance of one stereoisomer over the other isomer can be determined.

[0086] Chemical entities having carbon-carbon double bonds or carbon-nitrogen double bonds may exist in Z- or E- form (or cis- or trans- form). Furthermore, some chemical entities may exist in various tautomeric forms. Unless otherwise specified, chemical entities described herein are intended to include all Z-, E- and tautomeric forms as well.

[0087] The term “solvate” generally refers to a compound (e.g., free base) or a salt thereof, that further includes a stoichiometric or non- stoichiometric amount of solvent bound by non-covalent intermolecular forces. Wherein the solvent is water, the solvate is a hydrate.

[0088] The term “salt” or “pharmaceutically acceptable salt” refers to salts derived from a variety of organic and inorganic counter ions well known in the art. Pharmaceutically acceptable acid addition salts can be formed with inorganic acids and organic acids. Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like. Pharmaceutically acceptable base addition salts can be formed with inorganic and organic bases. Inorganic bases from which salts can be derived include, for example, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like. Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, specifically such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine. In some embodiments, the pharmaceutically acceptable base addition salt is chosen from ammonium, potassium, sodium, calcium, and magnesium salts.

[0089] The term “pharmaceutical composition” generally refers to a composition comprising a menin inhibitor, in particular ziftomenib, in combination with at least one additional pharmaceutically acceptable carrier. A “pharmaceutically acceptable carrier” refers to media generally accepted in the art for the delivery of biologically active agents to an individual, including, e.g., an adjuvant, an excipient or vehicle, such as diluents, preserving agents, fillers, flow regulating agents, disintegrating agents, wetting agents, emulsifying agents, suspending agents, sweetening agents, flavoring agents, perfuming agents, antibacterial agents, antifungal agents, lubricating agents and dispensing agents, depending on the nature of the mode of administration and dosage forms. Suitable carriers include without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye, colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier which has been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.

[0090] Pharmaceutical compounds are formulated according to several factors well within the purview of those of ordinary skill in the art. These include, without limitation: the type and nature of the active agent being formulated; the subject to which the agent-containing composition is to be administered; the intended route of administration of the composition; and the therapeutic indication being targeted. Pharmaceutically acceptable carriers include both aqueous and non- aqueous liquid media, as well as a variety of solid and semi-solid dosage forms. Such carriers can include a number of different ingredients and additives in addition to the active agent, such additional ingredients being included in the formulation for a variety of reasons, e.g., stabilization of the active agent, binders, etc., well known to those of ordinary skill in the art. Descriptions of suitable pharmaceutically acceptable carriers, and factors involved in their selection, are found in a variety of readily available sources such as, for example, Allen, L. V., Jr. et al., Remington: The Science and Practice of Pharmacy (2 Volumes), 22nd Edition, Pharmaceutical Press (2012).

[0091] As used herein, “treatment” or “treating” refers to an approach for obtaining beneficial or desired results with respect to a disease, disorder, or medical condition (e.g., AML) including but, in certain instances, not limited to a therapeutic benefit and/or a prophylactic benefit. Therapeutic benefit refers to eradication or amelioration of the underlying disorder being treated. A therapeutic benefit is also achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the individual, notwithstanding that the individual may still be afflicted with the underlying disorder. In certain embodiments, for prophylactic benefit, the compositions are administered to an individual at risk of developing a particular disease, or to an individual reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.

[0092] A “therapeutic effect,” as that term is used herein, encompasses a therapeutic benefit and/or a prophylactic benefit as described above. A prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.

[0093] As used herein, the term “effective amount” in connection with a compound means an amount capable of treating, preventing, or managing a disorder, disease, or condition, or one or more symptoms thereof.

[0094] As used herein, the term “prophylactic amount” in connection with a compound means an amount capable of preventing a disorder, disease, or condition, or one or more symptoms thereof, or reducing the ultimate severity of the disorder, disease, or condition, or of one or more symptoms thereof.

[0095] As used herein, the term “optimal biological dose” or “OBD” means the lowest dose of drug, such as an investigational drug, that provides the highest rate of efficacy while being safely administered.

[0096] As used herein, the term “recommended Phase 2 dose” means a dose of an investigational drug that has been accepted by a governmental authority (e.g., the U.S. Food and Drug Administration (FDA) or the similar authority in other countries) for evaluation in a Phase 2 study.

[0097] As used herein, the term “safe and effective dose” means a dose of a drug, such as an investigational drug, that provides a clinical effect without unacceptable side effects.

[0098] As used herein, the term “maximum tolerated dose” means the dose means the highest dose of a drug, such as an investigational drug, that does not cause unacceptable side effects, e.g., where the observed toxicity rate (e.g., dose-limiting toxicity rate) is less than 0.33.

[0099] A “breakthrough therapy designation” refers to the designation given by a governmental authority (e.g., the FDA or the similar authority in other countries) for an active pharmaceutical ingredient that treats a serious or life-threatening condition and for which preliminary clinical evidence (e.g., Phase 1 clinical data) indicates it may demonstrate substantial improvement on a clinically significant endpoint over available therapies. In the U.S., the status is referred to as breakthrough therapy designation; in Europe the status is Priority Medicine or PRIME. As used herein, a breakthrough therapy designation may be given for a particular indication and/or genetic sub-type, such as NPM1-m AML. [0100] An “investigational drug” is a substance that has been tested in laboratory experiments and has been approved by a governmental authority (e.g., the FDA or the similar authority in other countries) for testing in humans.

[0101] “Chemotherapy” means the administration of one or more chemotherapeutic drugs and/or other agents to an individual by various methods, including intravenous, oral, intramuscular, intraperitoneal, intravesical, subcutaneous, transdermal, buccal, or inhalation or in the form of a suppository. In the context of acute leukemia, chemotherapy is intensive chemotherapy, including a combination of an anthracycline, such as daunorubicin or idarubicin, and cytarabine, in a “7+3” regimen (cytarabine continuously for 7 days, along with short infusions of an anthracycline on each of the first 3 days).

[0102] “Individual” refers to an animal, such as a mammal, for example a human. The methods described herein can be useful in both human therapeutics and veterinary applications. In some embodiments, the individual is a mammal, and in some embodiments, the individual is human. “Mammal” includes humans and both domestic animals such as laboratory animals and household pets (e.g., cats, dogs, swine, cattle, sheep, goats, horses, rabbits), and non-domestic animals such as wildlife and the like. In some embodiments, the human is > 18 years of age. In some embodiments, the human is less than 18 years of age, less than 12 years of age, less than 6, 5, 4, 3, 2, or 1 year of age.

[0103] Clinical terms used herein include the following: “CR” means a complete remission, with no visible evidence of leukemia cells in blood or bone marrow, normal bone marrow function, and normal numbers of healthy blood cells having returned to circulation as confirmed by bone marrow biopsy and blood testing; the CR rate is defined as the population of patients achieving a best overall response of CR; “CRh” means a complete response with hematologic recovery; the CR/CRh response rate is defined as the proportion of patients achieving a best overall response of CR with or without MRD, or CRh; “CRi” means a complete response with incomplete hematologic recovery; “CRp” means complete remission with incomplete platelet recovery; CRc means composite complete remission and the response rate is defined as the proportion of patients achieving a best overall response of CRi (including CRp), CRh, or CR (including MRD-); “MRD” means measurable residual disease and refers to levels of leukemia that are not readily observed microscopically but can be detected by a laboratory method. A CR can be with or without measurable disease (CR MRD+/MRD-); “MLFS” means morphologic leukemic-free state; “PR” means partial response; “SD” means stable disease without progression; “ORR” means overall response rate and is determined by the formula, ORR = CR (including CR MRD-) + CRh + MLFS (including CRp).

[0104] “BC” means blast count and refers to the percentage of blasts in the bone marrow or blood. In normal bone marrow, the blast count is 5% or less, while the blood usually does not contain blasts. A level of at least 20% blasts in the marrow or blood usually indicates a diagnosis of AML.

[0105] Hydroxyurea, or hydrea, is an antimetabolite that prevents the excessive production of blood cells in proliferative diseases, and is useful in AML to reduce elevated levels of leukemic white blood cells.

[0106] “DS” means differentiation syndrome, a potentially serious side effect that may occur in patients with acute leukemia such as AML who have been treated with certain types of anticancer drugs. Differentiation syndrome usually occurs within 1-2 weeks after starting treatment. It is caused by large, rapid release of cytokines from leukemia cells that are affected by the anticancer drugs. Signs and symptoms of differentiation syndrome include fever, cough, difficulty breathing, weight gain, swelling of arms, legs, and neck, build-up of excess fluid around the heart and lungs, low blood pressure, and kidney failure.

[0107] “ SCT” or “HSCT” means hematopoietic stem cell transplant. In some embodiments of the methods provided herein, the subject receives an SCT after the treating or administering of ziftomenib or a pharmaceutically acceptable form thereof. In some embodiments of the methods provided herein, the subject has received an SCT prior to the treating or administration of ziftomenib or a pharmaceutically acceptable form thereof. In some embodiments, ziftomenib or a pharmaceutically acceptable form thereof is administered to a subject prior to an SCT and following the SCT (e.g., as maintenance therapy).

[0108] Extramedullary hematopoiesis is the formation and activation of blood cells outside the bone marrow, as a response to hematopoietic stress caused by leukemia.

[0109] The term “co-administration,” “administered in combination with,” and their grammatical equivalents, as used herein, encompass administration of two or more agents to an animal, including humans, so that both agents and/or their metabolites are present in the individual at the same time. Co-administration includes simultaneous administration in separate compositions, administration at different times in separate compositions, or administration in a composition in which both agents are present. [0110] The terms “antagonist” and “inhibitor” are used interchangeably, and they refer to a compound having the ability to inhibit a biological function (e.g., activity, expression, binding, protein-protein interaction) of a target protein (e.g., menin, MLL1, MLL2, and/or an MLL fusion protein). Accordingly, the terms “antagonist” and “inhibitor” are defined in the context of the biological role of the target protein. While preferred antagonists herein specifically interact with (e.g., bind to) the target, compounds that inhibit a biological activity of the target protein by interacting with other members of the signal transduction pathway of which the target protein is a member are also specifically included within this definition. A preferred biological activity inhibited by an antagonist is associated with the development, growth, or spread of a tumor.

[0111] The term “agonist” as used herein refers to a compound having the ability to initiate or enhance a biological function of a target protein, whether by inhibiting the activity or expression of the target protein. Accordingly, the term “agonist” is defined in the context of the biological role of the target polypeptide. While preferred agonists herein specifically interact with (e.g., bind to) the target, compounds that initiate or enhance a biological activity of the target polypeptide by interacting with other members of the signal transduction pathway of which the target polypeptide is a member are also specifically included within this definition.

[0112] “Signal transduction” is a process during which stimulatory or inhibitory signals are transmitted into and within a cell to elicit an intracellular response. A modulator of a signal transduction pathway refers to a compound which modulates the activity of one or more cellular proteins mapped to the same specific signal transduction pathway. A modulator may augment (agonist) or suppress (antagonist) the activity of a signaling molecule.

[0113] As used herein, a “sample” includes and/or refers to any fluid or liquid sample which is being analyzed in order to detect and/or quantify an analyte. In some embodiments, a sample is a biological sample. Examples of samples include without limitation a bodily fluid, an extract, a solution containing proteins and/or DNA, a cell extract, a cell lysate, or a tissue lysate. Non- limiting examples of bodily fluids include urine, saliva, blood, serum, plasma, cerebrospinal fluid, tears, semen, sweat, pleural effusion, liquified fecal matter, and lacrimal gland secretion.

[0114] The term “in vivo” refers to an event that takes place in an individual’s body.

[0115] The term “in vitro” refers to an event that takes places outside of an individual’s body. For example, an in vitro assay encompasses any assay run outside of an individual. In vitro assays encompass cell-based assays in which cells alive or dead are employed. In vitro assays also encompass a cell-free assay in which no intact cells are employed. [0116] As used herein, the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “include” and “includes”) or “containing” (and any form of containing, such as “contain” and “contains”), are inclusive or open-ended and do not exclude additional, unrecited elements or process steps. As also used herein, in any instance or embodiment described herein, “comprising” may be replaced with “consisting essentially of’ and/or “consisting of’, used herein, in any instance or embodiment described herein, “comprises” may be replaced with “consists essentially of’ and/or “consists of’.

[0117] As used herein, the term “and/or” is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example, “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each were set out individually herein.

[0118] As used herein, the term “about,” when used in connection with doses, amounts, or weight percentages, mean a dose, amount, or weight percent within 10%, or within 5%, or within 2%, or within 1% of the stated amount.

[0119] Where a numerical value is used herein, such a value may encompass a range that is ± 5% of the stated numerical value.

EXAMPLES

[0120] The following examples are included for illustrative purposes only and are not intended to limit the scope of the present disclosure.

Example 1 - Analysis of Ziftomenib Concentrations in Tissues and Plasma in Mice

[0121] The concentrations of ziftomenib in plasma, bone marrow, heart, and spleen were measured following 8-day oral gavage administration of ziftomenib in female C57BL/6 mice. A group of 5 animals was treated PO at 100 mg/kg of ziftomenib daily for 8 days. Bone marrow, spleen, plasma, and heart were sampled 24 hours post-Day 8 dose. Each sample was processed as follows:

Blood Collection and Processing: Each blood collection (about 0.03 mL) was performed from saphenous vein or other suitable site of each animal into pre-chilled commercial EDTA-K2 tubes or pre-chilled plastic microcentrifuge tubes containing 2 pL of 0.05 M EDTA-K2 as anti- coagulant and placed on wet ice until centrifugation. Blood samples were processed for plasma by centrifugation at approximately 4 °C at 3,200 x g for 10 min. Plasma was collected and transferred into pre-labeled 96-well plate or polypropylene tubes, quick-frozen over dry ice, and kept at -60 °C or lower until analysis. Analysis was performed by LC-MS/MS.

Tissue Processing: The tissue samples of drug level analysis were homogenized on wet ice using homogenizing buffer (MeOH/15 mM PBS 1 :2) at the ration of 1 :9 (1 g tissue with 9 mL buffer). The tissue-homogenate was stored at -60 °C or lower until analysis. Analysis was performed by LC-MS/MS.

As shown in Figure 1, the analyses showed that ziftomenib accumulates in tissues at high levels relative to plasma.

Example 2 - Plasma Protein Binding of Ziftomenib

[0122] Ziftomenib or the positive control, warfarin, were spiked into plasma from CD-I mouse and human. Ziftomenib was tested at concentrations of 0.2, 2, and 10 pM, and warfarin was tested at 2 uM. Spiked plasma samples were pre-incubated at 37 ± 1 °C and then centrifuged to pellet the plasma protein, enabling separation from the free compound in the supernatant. Concentrations of ziftomenib and warfarin in the spiked plasma and the supernatant samples were determined using LC-MS/MS. The % Unbound, % Bound, and % Remaining were calculated according to the following equations: where [F] is free compound concentration or peak area ration of analyte/intemal standard of protein-free sample after ultracentrifugation; [TO] is compound concentration or peak area ratio of analyte/intemal standard in plasma at time zero; [T4.5] is compound concentration or peak area ratio of analyte/intemal standard in plasma after incubation for 4.5 hours.

Ziftomenib plasma protein binding was determined to be more than 99%. Example 3 - A Phase 1/2 First-in-Human Study of the Menin-MLL(KMT2A) inhibitor KO- 539 (Ziftomenib) in Patients with Relapsed or Refractory (R/R) Acute Myeloid Leukemia (AML) (NCT 04067336)

A. Background

[0123] KO-MEN-OOl is a first-in-human, open-label, multiple-cohort study of ziftomenib in adult patients with R/R AML that includes an initial dose-escalation portion (Phase la) and a dose- validation/cohort expansion portion (Phase lb).

[0124] The Phase la dose escalation trial enrolled 30 adult patients with R/R AML regardless of genotype (all-comer population). Patients received 50 mg (1), 100 mg (1), 200 mg (6), 400 mg (5), 600 mg (5), 800 mg (11), or 1000 mg (1) ziftomenib once daily to assess safety, tolerability, and anti-leukemic activity (CR/CRh, CR with and without measurable residual disease (MRD), duration of remission (DOR), event-free survival, and overall survival (OS)) at a range of ziftomenib dose levels, and to determine the maximum tolerated dose (MTD) and/or the recommended Phase 2 dose (RP2D) (optimal biologically effective dose) of ziftomenib in patients with R/R AML, irrespective of genotype. The median age of the subjects was 65.5 years (range, 22-85), 33% (10) had KMT2A-r AML and 13% (4) had NPM1-m AML (non-KMT2A-rlNPM1-m, 16 (53%)). Patients were heavily pre-treated and had a median of 3.5 prior therapies (range, 1-9), most having received prior venetoclax, with 23% having > 1 prior stem cell transplant (SCT).

[0125] The Phase lb dose-validation portion of the study explored the two lowest doses from the Phase la portion that had demonstrated meaningful activity, 200 mg and 600 mg, ziftomenib once daily, in KMT2A-r or NPM1-m AML to investigate the possibility of an optimal biologically active dose for these patient populations. The median age of subjects among the first 36 subjects enrolled (NPM1-m, 17; KMT2A-r, 19; plus co-mutations including IDH and FL T3 predominantly for NPM1-m patients) was 52 years (range, 28-84), and approximately one-third had at least one prior SCT. The patients had a median of 3 prior therapies (range, e.g., 1 to 12 for KMT2A-r and 2 to 8 for NPM1-m for first 24 patients), with 66.7% of patients having been treated with venetoclax prior to enrollment and 30.6% having had SCT.

[0126] Cumulative of the first 53 patients in Phase lb, demographics are shown in Table 1.

Table 1.

* Patient could have both FLT3 and IDH1/2 and be counted in both co-mutation categories.

[0127] For 53 patients in Phase lb, with patients either going off study within the first cycle, or having received treatment for at least one cycle, patient disposition is shown in Table 2.

Table 2.

** No adverse events were considered treatment related.

Approximately 30% of patients were still on therapy and almost 50% still in follow-up. Patients most often discontinued due to progression of underlying disease. While six patients discontinued due to an adverse event, none of those were considered to be treatment related.

[0128] In both parts, ziftomenib was dosed orally, once daily, in 28-day cycles.

Study Participants - Populations Analyzed

[0129] The population for clinical safety and efficacy analysis in this Phase 1 study was a Modified Intent-to-Treat (mITT) population: All patients who received at least 1 dose of study drug. Patients were grouped in the mITT population according to dosing cohort and tumor genetics. The following subgroups were used in the analysis:

• KMT2A-r subgroups for the 200 mg and 600 mg dose cohorts in mITT Phase la and Phase lb combined, and

• NPM1-m subgroups for the 200 mg and 600 mg dose cohorts in mITT Phase la and Phase lb combined. [0130] Where appropriate, data is presented in this example for the following patient subgroupings from the analysis populations:

• Group 1 : Phase la (all patients in mITT Set at time of data cut),

• Group 2: Phase lb (all patients in mITT Set at time of data cut),

• Group 3: Phase la on-target mutation patients (e.g., patients with KMT2A -r or NPM1-vn AML) plus all patients in mITT Set of Phase lb at time of data cut (all on-target cohort), and

• Group 4: Phase la on-target mutation patients plus the first 24 patients (or up to 53 total, if specified) enrolled in Phase lb (on-target mature cohort) who had been followed for a minimum of 2 months.

These patient groupings allow for the assessment of safety for patients regardless of mutational status (Group 1), safety and efficacy in the on-target patient population (Groups 2-4), and signals of efficacy in patients to support determination of the RP2D and who have had sufficient time on treatment to allow for potential clinical benefit/response (Group 4).

B. Anti -Leukemic Activity

[0131] In the Phase la portion of the study, across genotypes evaluated, clinical benefit was demonstrated, with 30% of R/R AML patients remaining on treatment for at least four cycles, and with disease control (e.g., decreasing blast counts [BC] or decreased hydroxyurea (hydrea) requirements), and overall improvement in patient performance status observed across all dose levels. At 100 mg, one complete remission (CR) was observed in a patient with SETD2 and RUNX1 mutations, indicating likely dependence of other AML genotypes on the menin pathway. At 200 mg, the two NPM1-vn patients responded positively: one patient experienced a CR without measurable residual disease [MRD-] for at least 100 weeks’ duration, and one patient with NPM1- m and a FLT3-ITD mutation achieved a morphologic leukemic-free state [MLFS]). At the 600 mg and 800 mg doses, KMT2A-r patients experienced stable disease with significantly decreased BC and improved performance status of significant duration (e.g., one patient with response lasting more than four months). Observed clinical benefits from the Phase la part included: 29% remaining on treatment for at least four cycles, decreasing blast counts (RUNX1 mutation), decreasing hydroxyurea (hydrea) requirements (one KMT2A-r subject), and overall improvement in patient performance status across dose levels. [0132] Clinical efficacy in the Phase lb segment of the trial was dose dependent. The response rates consistently showed increased anti-leukemic activity at the 600 mg dose once daily (QD) compared to the 200 mg dose QD. The complete remission (CR)/CR with partial hematologic recovery (CRh) and composite CR rates in on-target patients in Phase la and the first 24 patients enrolled in Phase lb at 600 mg versus 200 mg were 21.4% and 6.7% (la) and 28.6% versus 6.7% (la and 24 lb), respectively. At 200 mg, changes in bone marrow morphology and stable/decreasing blast counts were seen. Three patients were dose-escalated to 600 mg with improvement: one achieved a bone marrow blast count < 5% and a significant reduction of high burden extramedullary disease despite persistence of a small disease focus; one had significantly reduced BC and disease control; one attained MLFS and remained on treatment. At 600 mg, 25% of the first 24 Phase lb patients had a best response of CR or CR with partial hematologic recovery (CRh), including 33.3% of NPM1-m patients achieved CR or CRh. For the first 24 Phase lb patients, the composite CR was 33% with 75% measurable residual disease (MRD), and the overall response rate (ORR) was 42%.

[0133] As of October 2022, Phase lb enrollment was completed (N=53) and 30% (including 21% at the 600 mg dose) were still undergoing treatment with evolving clinical benefit. While the 200 mg dose showed some efficacy for the NPM1-m patient population, the KMT2A-r patients did not exhibit any formal responses. The overall efficacy signals are shown in Table 3, with an overall CR/CRh of 21.2%, CRc of 26.3%, and an ORR of 28.9% in the pooled groups. Within this expanded patient group, a total of 20 NPM1-m patients were enrolled and treated with ziftomenib 600 mg. This subgroup continued to demonstrate strong evidence of anti-leukemic activity, with a CR/CRh of 30.0%, a CRc of 35.0%, and an ORR of 40.0%. While 43% of patients that achieved a CRc also achieved MRD negativity, only five of those were tested for MRD. Of those patients tested, 60% were MRD negative. Of the CR/CRh patients, two-thirds had IDH and/or FTL3 co-mutations. Overall, of seven patients with IDH co-mutations, 57% had a CR on ziftomenib. In addition, across groups, patients who experienced differentiation syndrome had an ORR of 75%. Although significant activity was observed in KMT2A-r patients, a formal CR/CRh response was achieved in only one patient, to give an ORR of 16.7%. Table 3. Summary of Response for All On-Target Mutation 200 mg and 600 mg Patients

Treated — 58 patients from Phase la/lb n/N = number of patients; MRD was assessed for 5/7 CRc patients; 3 of those patients (60%) tested were MRD negative; CRc includes CR, CRh, CRi, CRp; ORR includes CR, CRh, CRi, CRp, MLFS.

C. Safety and Tolerability

• Safety and Tolerability by Dose

[0134] There was no apparent relationship between ziftomenib dose and the rate of treatment- emergent adverse events (TEAEs), regardless of severity, seriousness, or relatedness. Overall, events were consistent with effects of underlying disease. Incidence rates for TEAEs and serious adverse events (SAEs) are shown in Table 4. While there were numerical differences between dosing groups, there was no significant increase in rate or severity of AEs with increasing dose.

Table 4. Summary of Patient Incidence of Adverse Events -mlTT

Abbreviations.: AE = adverse event; MedDRA = Medical Dictionary for Regulatory Activities; mlTT = modified intent-to-treat: n/N = number of patients:

NG-CTCAE = National Cancer Institute Common Terminology Criteria for Adverse Events; SAE = serious adverse event; TEAE = treatment-emergent adverse event

Adverse events are coded using MedDRA dictionary, Version 24.0.

TEAE is defined as adverse event with an onset date on or after the first dose of study drug, and before 28 days after the last dose of study drug. An adverse event collected after 28 days of the last dose of study drug is not counted as TEAE and is displayed only in AE listing(s).

Treatment-related adverse event is an adverse event that has relationship to study drug KO-539 designated by the investigator as Related.

Adverse events are evaluated based on NCI-CTCAE (version 5.0).

[0135] The most frequent TEAEs reported by > 15% of patients across Phases la and lb were similar and included diarrhea, anemia, nausea, increased blood creatinine, fatigue, pneumonia, increased alanine aminotransferase, arthralgia, increased aspartate aminotransferase, decreased appetite, peripheral edema, pyrexia, anemia, epistaxis, febrile neutropenia, hypomagnesemia, and differentiation syndrome.

• TEAEs by Severity (> Grade 3)

[0136] In Phase la, 11 of 11 patients (100%) reported at least one TEAE, with 26 of 30 patients (86.7%) reporting TEAEs > Grade 3 regardless of causality. The most common TEAEs > Grade 3 were anemia (8 patients [26.7%]), pneumonia (7 patients [23.3%]), followed by febrile neutropenia, neutropenia, thrombocytopenia, and decreased appetite (3 patients each [10.0%]). Eight patients (26.7%) reported > Grade 3 TEAEs considered by the Investigator to be related to ziftomenib (1 each at 50 mg, 100 mg, 200 mg, 400 mg, 600 mg, and 1000 mg, and 2 at 800 mg). The most common > Grade 3 ziftom enib-related TEAE reported in patients in Phase la was pulmonary embolism (2 patients [6.7%]). TEAEs > Grade 3 by dose for Phase la are shown in Table 5.

Table 5. > Grade 3 TEAEs (All Causality)

[0137] Two dose-limiting toxicities occurred: pneumonitis (400 mg dose) and differentiation syndrome (1000 mg dose). No drug-induced QT/QTc prolongation was reported in Phase la. Two DLTs were reported: (1) 400 mg cohort (pneumonitis, post-aspiration pneumonia); (2) 1000 mg cohort (differentiation syndrome).

[0138] For the first 24 patients in the Phase lb portion of the study, TEAEs of > Grade 3 that occurred in > 10% of all patients (N=24) were anemia, febrile neutropenia, neutropenia, and thrombocytopenia (25% each); differentiation syndrome (DS) and leukocytosis (17% each); and sepsis and leukopenia (13% each). At 200 mg (N=12), TEAEs of > Grade 3 that occurred in > 10% of patients were neutropenia and thrombocytopenia (33% each); febrile neutropenia, anemia, and sepsis (25% each); and DS, leukocytosis, and respiratory failure (17% each). At 600 mg (N=12), TEAEs of > Grade 3 that occurred in > 10% of patients were febrile neutropenia and anemia (25% each); and DS, leukocytosis, neutropenia, thrombocytopenia, leukopenia, and diarrhea (17% each).

[0139] For the first 36 patients in Phase lb, 34 of 36 patients (94.4%) reported at least 1 TEAE, with 28 patients (77.8%) reporting > Grade 3 TEAEs regardless of causality. The most common TEAEs > Grade 3 were febrile neutropenia (7 patients [19.4%]), DS and anemia (6 patients each [16.7%]), and pneumonia, sepsis, and platelet count decreased (4 patients each [11.1%]). Fifteen patients (41.7%) reported > Grade 3 TEAEs considered by the Investigator to be related to ziftomenib, including 7 patients (41.2%) in the 200 mg cohort, and 8 patients (42.1%) in the 600 mg cohort. The most common > Grade 3 ziftomenib-related TEAE reported in patients in Phase lb was DS (6 patients [16.7%]). SAEs regardless of causality were reported by 23 patients (63.9%), and 11 patients (30.6%) reported SAEs considered by the Investigator to be related to ziftomenib (5 patients [29.4%] in the 200 mg cohort and 6 patients [31.6%] in the 600 mg cohort). No patient reported a TEAE requiring dose reduction and the rate of patients requiring dose interruptions or treatment discontinuation was also similar between the 200 mg and 600 mg ziftomenib dose levels (41.2% vs 31.6% and 11.8% vs 10.5%, respectively). Serious adverse events determined to be related to ziftomenib included DS (4 patients), increased alanine aminotransferase (1 patient), and pleuritic chest pain (1 patient) at 200 mg, and myocarditis (1 patient), DS (2 patients), febrile neutropenia (2 patients), worsening dyspnea (1 patient), leukocytosis (1 patient), cardiomyopathy (1 patient), diarrhea (1 patient), and dehydration (1 patient) at 600 mg.

[0140] In the 53 subjects in the Phase lb portion, few adverse events, regardless of causality, that were Grade 3 or above occurred in more than 10% of patients. TEAEs > Grade 3 that occurred in > 10% of all patients (N=24) were anemia, febrile neutropenia, neutropenia, and thrombocytopenia (25% each); differentiation syndrome and leukocytosis (17% each); and sepsis and leukopenia (13% each). At 200 mg (N=12), TEAEs > Grade 3 that occurred in > 10% of patients were neutropenia and thrombocytopenia (33% each); febrile neutropenia, anemia, and sepsis (25% each); and differentiation syndrome, leukocytosis, and respiratory failure (17% each). At 600 mg (N=12), TEAEs > Grade 3 that occurred in > 10% of patients were febrile neutropenia and anemia (25% each); and differentiation syndrome, leukocytosis, neutropenia, thrombocytopenia, leukopenia, and diarrhea (17% each).

[0141] No reports of QTc prolongation were noted in Phase lb and, overall, no clinically meaningful trends in clinical laboratory assessments, vital signs, or ECGs were observed.

[0142] In summary, the safety data collected during Phase lb as of the data cut-off that pooled 36 patients were consistent with the data from Phase la, which suggest comparable safety and tolerability between 200 mg and 600 mg ziftomenib monotherapy doses.

• Safety and Tolerability by Genotype

[0143] When evaluated by genetic subtype, the safety results for KMT2A -r and NPM1-m AML patients who received 200 mg or 600 mg across Phase la and lb (Table 6) were generally consistent with the overall study population, which showed no apparent relationship between ziftomenib dose and the overall frequency of TEAEs. The most common TEAEs > Grade 3 were anemia, febrile neutropenia, pneumonia, sepsis, increased alanine aminotransferase, decreased platelet count, and differentiation syndrome for KMT2A-r, and anemia, neutropenia, thrombocytopenia, diarrhea, pneumonia, sepsis, decreased neutrophil count, decreased white blood cell count, and hyperglycemia for NPM1-m. However, the risk of severe adverse events was elevated for the KMT2A-r cohort at 70.8% as compared to a rate of 52.9% for NPM1-r. Serious adverse events that occurred in > 10% of all patients included febrile neutropenia (25.0%), pneumonia (12.5%), sepsis (12.5%), and DS (20.8%) for KMT2A-r. and Clostridium difficile infection (11.8%), pneumonia (11.8%), and sepsis (11.8%) for NPM1-m, and the rates were not dose-dependent. Dose-limiting toxicities occurred at a rate of 30.0% for KMT2A-r, and at a rate of 14.3% for NPM1-m.

Table 6. Summary of Patient Incidence of Adverse Events by Genotype - Phase la and

Phase lb Combined - mITT Set

Abbreviations: See Table 4.

[0144] For each of the AE categories (TEAEs, Grade 3+ TEAEs, and SAEs), the rates of reported events and severity were consistent between dose groups. Taken together with a limited number of TEAE-related dose interruptions and/or discontinuations, the data indicate that ziftomenib tolerability does not decrease with increasing dose, and comparable safety and tolerability between 200 mg and 600 mg ziftomenib doses. When evaluated by genetic subtypes, the safety results for KMT2A-r and NPM1-m AML patients who received 200 mg or 600 mg were generally consistent with the overall study population and showed no apparent relationship between ziftomenib dose and the overall frequency of TEAEs. With the exception of DS, discussed further below, reported events appeared to be general in nature or related to underlying disease.

• Differentiation Syndrome

[0145] Given inhibition of menin activity disrupts gene expression pathways responsible for maintaining the pathologic dedifferentiated stem cell-like phenotype of KMT2A-r and NPM1-m AML, the TEAE of DS is considered treatment-related and due to the effect of ziftomenib on cancer cells. DS responses must be carefully managed to ensure patient safety and continued access to therapy.

[0146] In Phase la, a single event of the on-target effect of DS (Grade 4) was reported in a KMT2A-r patient at the 1000 mg dose level, resulting in de-escalation of the 1000 mg dose cohort and completion of enrollment of Phase la at the 800 mg dose. Among the first 24 patients in Phase lb, DS occurred in seven patients, including three KMT2A-r patients at 200 mg, of which two had events > Grade 3 including one death, and four patients at 600 mg, of whom two experienced Grade 3 DS (one KMT2A-r and one NPM1-m and two were Grade 2 (one KMT2A- r and one NPM1-m). DS guidance was developed, and implementation led to a reduction in reported DS event severity.

[0147] Review of all data for potential events of DS that may not have been identified by Investigators was performed to apply the Norsworthy Algorithm (Norsworthy, 2020), and those data are tabulated along with Investigator-identified cases in Table 7. As shown in Table 7, among the first 36 patients in Phase lb, the rate of Investigator-reported DS was consistent between the 200 mg and 600 mg dose levels (29.4% versus 26.3%, respectively). The rate of severe DS in Phase lb was higher at the 200 mg dose level, with 23.5% of patients reporting >Grade 3 DS compared to 10.5% at the 600 mg dose level, suggesting DS severity does not increase with dose.

Table 7. Differentiation Syndrome in Phase lb - mITT Set

Abbreviations: DS = differentiation syndrome; n/N = number of patients; Pts = patients.

[0148] Although the general safety profile for each genetic cohort was consistent across the overall study population and was not dose-dependent, a genetic subtype-dependency for DS was observed, as shown in Table 8, with KMT2A-r patients being more likely to experience the event. Out of 10 total DS cases reported as of the 36-patient timepoint of Phase lb, 7 (70.0%) occurred in KMT2A-r patients, suggesting that KMT2A-r patients are potentially more susceptible to DS- type events. In addition, KMT2A-r patients reported an increased rate of severe DS compared to the NPM1 -m subgroup overall (20.8% for KMT2A-r vs 5.9% for NPM1-m) and at the 200 mg and 600 mg ziftomenib dose levels, respectively. Where DS occurred in NPM1-m subjects, it was generally moderate in severity and resolved with appropriate intervention.

Table 8. Differentiation Syndrome in Phase la and Phase lb by Genotype at the 200 mg and

600 mg Ziftomenib Dose Levels- mITT Set

Abbreviations: See previous tables.

[0149] Grade 3+ TEAEs occurring in > 10% of participants (regardless of causal assessment) in Phase lb by genetic subtype and dose are shown in Table 9 for the 53-subject group. Few adverse events, regardless of causality, that were Grade 3 or above occurred in more than 10% of patients. None were reported in the NPM1-m population. For KMT2A-r patients, 25% reported differentiation syndrome and 13% febrile neutropenia at the 600 mg dose.

Table 9.

[0150] Incidence and severity of differentiation syndrome across 53 subjects in Phase la/lb for the 200 mg and 600 mg doses by genotype are shown in Table 10.

Table 10.

As shown above, 20% of NPM1-m patients treated at 600 mg experienced differentiation syndrome with one quarter of those being at least Grade 3. For KMT2A-r patients, rates were similar across doses, with about 38% of patients experiencing differentiation syndrome and 25- 30% experiencing Grade 3 or higher events. Patients with a differentiation syndrome event at 600 mg had an ORR rate of 75% for NPM1-m and 16.7% for KMT2A-r.

[0151] There were additional, less commonly reported, adverse events (alanine aminotransferase increase, pleuritic chest pain, myocarditis) that may have been related to DS events. These adverse events occurred almost exclusively in KMT2A-r patients. Because KMT2A- r disease is often monocytic and therefore invasive, it may be associated with extramedullary disease that is not always recognized at baseline. (Fianchi et al., Mediterr. J. Hematol Infect Dis. 2021, 13(1), e2021030.) Because ziftomenib concentrates in tissue, it is therefore possible and suspected that these events are related to a ziftom enib-induced differentiation of leukemic cells in the associated extramedullary sites of disease and not an indication of disease progression.

[0152] These data suggest differentiation syndrome represents the most significant adverse effect associated with ziftomenib therapy. It does not show evidence of dose dependence, however there is a clear association with KMT2A-r disease versus NPM1-m AML. In the genetically enriched Phase lb population, DS was seen, not in a dose dependent manner, but in a genetic subtype-dependent manner with KMT2A-r patients being more likely to experience the event. It is suspected that due to the monocytic and therefore invasive nature of KMT2A-r leukemia, that these patients have higher degrees of undiagnosed extramedullary disease and associated increased levels of organ involvement (including heart, liver and other organs). Menin inhibitor-related DS, such as that induced by ziftomenib, has not been previously reported, and can manifest as bone pain, transient pain in extremities, initial elevation in liver function tests, cardiac inflammatory events and other temporary changes in organ function, all potentially related to differentiation of previously unrecognized extramedullary disease. This concept is supported by the well-known invasiveness of monocytic disease and the high levels of extramedullary involvement in KMT2A-r patients vs AML patients with other genotypes. (Kapur et al., Leuk. Res. Rep. 2022, 18, 100349.)

[0153] At the time of application filing, Phase lb enrollment was completed (N=53) and 21% (all at the 600 mg dose) were still ongoing treatment with evolving clinical benefit. The overall safety profile in the expanded group was consistent with that described above. No new DS cases had been reported or detected via the DS algorithm since the last data cut-off (N = 3 data set/4 safety database) among NPM1-m subjects.

[0154] The discoveries made during the study informed the development of treatment strategies to maximize time on treatment for patients. Notably, it was demonstrated that hyperleukocytosis was often incorrectly interpreted as disease progression or DS, and changes in peripheral blasts similarly were not predictive. Control of DS episodes was linked with a higher likelihood of clinical benefit. Although infrequent, when the event was seen in NPM1-m patients, it was manageable with modified DS monitoring and treatment practices, was resolved quickly, and often predicted a patient’s clearance of leukemia (-75% of NPM1-m patients with a DS event attained a CR/CRh/CRi (ORR), in part by allowing patients to continue treatment for at least two cycles. The advent of specific DS monitoring and treatment strategies helped to identify a unique menin inhibitor-associated presentation of DS and to address it in a way that enabled patients to remain on therapy.

D. Blood Chemistry

[0155] Mean change from baseline in Cycle 1 (28 days) for peripheral blasts and white blood cells for the on-target population at 600 mg (Phase la and lb) showed transient increases in these blood chemistry markers over the first one to two weeks, followed by reductions in these markers during the remainder of the first cycle, as shown in Figure 2. While not always associated with a DS event, or predictive of progression, early rises in white blood cell (WBC) counts and peripheral blasts appeared to correlate with drug activity, providing context for the rapid onset of DS-type symptoms after treatment initiation. The recognition that DS symptoms were indicative of drug effect led to implementation of mitigation procedures to allow patients to remain on treatment. While managed DS can be predictive of patient response, with 75% and 17% of NPMl-m and KMT2A-r patients, respectively, with DS ultimately achieving an ORR event, differences in severity of DS between the genetic subtypes were observed. The different responses may be due to the disseminated nature of KMT2A-r disease, which has widespread infiltration into extramedullary spaces. As shown in Example 1, ziftomenib accumulates in tissues at high levels. This high tissue penetrance may produce the diffuse and unpredictable DS symptomology reported in KMT2A-r patients (e.g., diffuse pain). Implementation of DS guidance led to better identification of DS events and earlier intervention.

E. Exposure and Biomarkers

[0156] Intensive or sparse pharmacokinetic sampling was conducted after the first dose (Cycle 1, Day 1) and at steady state (Cycle 2, Day 1). Steady state trough samples (pre-dose) were collected on Days 8 and 15 of Cycle 1 and where possible, in subsequent cycles. Concentrations of ziftomenib and certain active metabolites were measured by a validated liquid chromatography/mass spectrometry assay. The following parameters were determined: AUC0-24- ss (area under the plasma concentration-time curve over a dosing interval at steady state), C _trough -ss (trough plasma concentration measured at the end of the dosing interval at steady state), and C _max - ss (maximum concentration at steady state). Exposure-response analyses were performed for subjects who received at least 21 doses in the first cycle, using ORR (defined as MLFS, Cri [including CRp], CRh, or CR +/-MRD-) as the efficacy endpoint to determine the exposure/efficacy relationship. As shown in Figure 3, Panels A-C, dose-dependent increases in exposure with the 600 mg dose over the 200 mg dose were observed. However, ziftomenib exposures at the 600 mg and 800 mg doses were comparable. Based on these studies, any further increase in dose above 600 mg QD is not expected to increase the probability or extent of response. [0157] The change iISl expression at Cycle 1, Day 28, was measured as a pharmacodynamic biomarker of ziftomenib inhibition of menin transcriptional signaling. Evaluation of MEIS1 expression levels was performed on bone marrow aspirate samples taken during screening and at the end of Cycle 1 dosing with ziftomenib. The change in MEIS1 expression was determined using quantitative ribonucleic acid sequencing. Patients who received a CR by the time of the bone marrow biopsy were not assessed because MEIS1 expression is expected to be low due to the absence of leukemia cells. As shown in Figure 4A, MEIS1 expression was reduced by more than 85% at the end of Cycle 1 in four patients dosed at 600 mg, while no reduction was detected for two patients dosed at 200 mg. As shown in Figure 4B, MEIS1 expression was 6- and 8-fold lower at Cycle 1, Day 28, in KMT2A-r and NPM1-m patients, respectively, dosed at 600 mg relative to 200 mg. Target gene expression at the 800 mg dose did not provide evidence of further knockdown.

[0158] Additionally, the expression of other menin target genes, such as H0XA9, HOXA10, and MEF2C, were 2- to 6-fold lower at 600 mg than at 200 mg. RNAseq data showing stronger inhibition of the menin pathway at 600 mg provides supportive evidence for 600 mg dosing over 200 mg.

[0159] Population pharmacokinetic analysis determined co-administration of CYP3A4 inhibitors, renal or hepatic status, patient mutation, and ECOG status were not significant covariates affecting pharmacokinetics.

F. Supplemental Clinical Study Data

[0160] Supplement 1.

[0161] This report provides updates on the Ph 1 NPMl-m patients dosed at the 600 mg RP2D (n=20) and on duration of remission (DoR) for a patient dosed at 200 mg, as of 31 JAN2023. The median age for patients treated at the 600 mg RP2D was 70.5 years (22 to 86y). FLT3 and IDH1/2 mutations were common (35% with FLT3 and 30% with IDH1/2, respectively); 20% harbored concurrent FLT3 and IDH1/2 co-mutations. The median number of prior therapies was 2.5 (r: 1 to 8), including 15% with >1 prior stem cell transplant (SCT) and 60% with prior venetoclax.

[0162] The cumulative safety profile for the ziftomenib 600 mg RP2D is consistent with prior reports, with no new signals observed. Most subjects (85%) had at least one > Grade 3 treatment- emergent adverse event (TEAE), with 30% of TEAEs considered potentially treatment-related. The most frequent (>10%) TEAEs > Grade 3 were anemia (25%), pneumonia (20%), thrombocytopenia, neutropenia and hyperglycemia (15% each). Among the NPMl-m patients, 20% reported any grade differentiation syndrome (DS) events, and 5% (n = 1) experienced Grade 3 DS.

[0163] As of 31JAN2023, the complete remission (CR) rate for NPMl-m patients treated with 600 mg was 30% (6 patients; 95% CI 12-54%), the CR and CR/CRh rates were both 30% (6 patients, 95% CI 12-54%), the composite CR rate (CRc; CR + CRh + CRi) was 35% (7 patients; 95% CI 15-59%), the MRD negativity rate was 43% (3 patients, 95% CI 10-82%; 5 of 7 patients achieving CRc were evaluated for MRD; off those evaluated, 60% were MRD negative), and the ORR rate was 40% (8 patients; 95% CI 19-64%). The median DoR for patients achieving CRc, which continues to mature, was 8.2 months per Kaplan-Meier (KM) estimate (95% CI: 1.5 to NE). One CR was noted at the 200 mg dose with an ongoing DoR of 32 cycles. Median time to CR for NPMl-m patients at RP2D was 70 days (r: 26 to 89). Two patients (1 CR and 1 CR with incomplete hematologic recovery [CRi]) proceeded to SCT and both remained in remission as of the cutoff. Median overall survival for NPMl-m patients treated with 600 mg was 5.1 months (95% CI: 2.1 to NE), with a median duration of follow-up of 8.0 months. As of the cutoff, 57.1% of patients achieving CRc at RP2D remained on treatment or in post-SCT follow-up; those on treatment continued to show evidence of evolving responses.

[0164] Ziftomenib at 600 mg continued to demonstrate significant clinical activity in heavily pretreated and co-mutated R/R NPMl-m AML patients. The safety profile remained consistent with previous reports and the on-target effect of DS continued to be manageable. Data suggest durable remissions as the DoR continues to mature with 5 of 8 patients with CRc (4 of 7 at 600 mg and 1 CR at 200 mg) ongoing at the cutoff. A single-arm registration-directed Phase 2 study is currently accruing to further evaluate ziftomenib monotherapy in R/R NPMl-m AML.

[0165] Supplement 2. This report provides an update on the Phase 1 NPM1-m patients from Phase la and lb, with emphasis on those dosed at the 600 mg RP2D (N=20) as of 12APR2023. Median age of the 600 mg RP2D patients was 70.5 years (range, 22 to 86y). FLT3 (30%) and IDH1/2 (40%) co-mutations were common (20% had both co-mutations). Median number of prior therapies was 3.0 (range, 1 to 10); 20% had >1 prior stem cell transplant (SCT). Patient baseline characteristics for Phase IB are shown in Table 11.

Table 11.

Notes: Data cut off: April 12, 2023. ^a Patient could have both FLT3 and IDH1/2 and be counted in both co-mutation categories. Additional reasons for treatment discontinuation include physician decision, receipt of alternative anticancer treatment, withdrawal by subject, and other. ^b All adverse events leading to discontinuation were not considered study drug related. Additional Reasons for study discontinuation include withdrawal by subject and completed. ECOG, Eastern Cooperative Oncology Group; FLT3, fms-like tyrosine kinase 3; IDH, isocitrate dehydrogenase; PS, performance score; SCT, stem cell transplant.

[0166] Based on updated results, the complete remission (CR) rate for NPM1-m patients at 600 mg was 35%, with 40% of patients overall achieving composite CR (CRc) and ORR of 45%. The median time to first response was 51 days (r: 26 to 225). One CR at the 200 mg dose had an ongoing DoR of 35 cycles. The median DoR for all NPM1-m patients achieving CRc was 8.2 months per Kaplan-Meier estimate (95% CI: 1.0 to NE). Two patients (1 CR and 1 CRi) underwent SCT and remained in remission as of the cutoff, one on post-SCT ziftomenib maintenance therapy. Median duration of remission was 8.2 months.

[0167] Molecular analyses suggest ziftomenib leads to measurable residual disease (MRD) clearance of target mutations such as NPM1, and co-mutations (e.g., FLT3 and IDH1 likely by targeting the founding clone and subclonal events or through targeting aberrant gene expression, as at least 2 patients with FLT3 and IDH1 co-mutations present at baseline were undetectable after

2 cycles. Data are shown in Table 12.

Table 12.

Notes: ^a Complete remission is defined as <5% bone marrow blasts with complete hematologic recovery and includes CRmrd, CRmrd-, and CR without MRD assessment. ^b CR/CRh includes complete remission and CRh. ^c CRc is defined as achieving best overall response of any of the following: CR (including CRmrd, CRmrd-, and CR without MRD assessment), CRh, CRi (including CRp). ^d In patients with NPM1-m, 6 of 8 patients were assessed for MRD; therefore, 66.7% of patients tested were MRD negative. MRD negativity rate is based on number of patients who had CRc, ORR, complete remission, or CR/CRh. ^e Overall response is defined as achieving best overall response of any of the following: MLFS, CRi (including CRp), CRh, CR (including CRmrd, CRmrd-, and CR without MRD assessment). 95% CI is based on Clopper- Pearson method. Efficacy set contains all subjects from mITT who had at least one post-baseline response assessment, or patients who died or ended study prior to first response assessment. CI, confidence interval; CR, complete remission; CRc, composite complete remission;

CRh, complete remission with partial hematological recovery; CRi, complete remission with incomplete hematologic recovery; CRmrd-, complete remission without measurable residual disease; CRp, complete remission with incomplete platelet recovery; KMT2A-r, lysine[K]- specific methyltransferase 2A-rearrangement; mITT, modified intent to treat; MRD, measurable residual disease; MLFS, morphological leukemia-free state; ORR, overall response rate; NPM1- m, nucleophosmin 1 -mutation.

[0168] Most patients (85%) had at least one > Grade 3 treatment-emergent adverse event (TEAE); 30% were potentially treatment-related. The most frequent (>20%) TEAEs > Grade 3 were anemia (25%) and thrombocytopenia (20%). Any grade differentiation syndrome (DS) was reported in 20%; most (n=3) were Grade 2.

[0169] The resistance profile was explored and the resistance mutation MEN1-M327I was found to develop in 1 of 29 patients (3.4%), detected at C4D28; the patient maintained stable disease through cycle 7.

[0170] In summary, ziftomenib continued to demonstrate significant clinical activity in heavily pretreated and co-mutated R/RNPMl-m AML patients where 35% of patients achieved CR. The safety profile remained consistent with prior reports, and episodes of DS were clinically manageable. Data revealed that remissions are durable, with MRD clearance of NPM1 and key co-mutations. Resistance mutations were detected infrequently, and ziftomenib was shown to remain effective against a common menin gatekeeper mutation.

[0171] Supplement 3. This report provides an update on the Ph 1 study of ziftomenib in AML patients as of 30 August 2023 (cutoff date). Patient demographics remained the same as reported in Table 11. No patients remained on treatment and 4 patients remained on study as of the cutoff date. Treatment was discontinued due to adverse event (5, 25%), death (1, 5%), physician decision (1, 5%), disease progression as assessed by investigator (9, 45%), receipt of alternative anticancer treatment (1, 5%), and other (2, 10%). Patient participation in the study was discontinued due to completion (1, 5%) or death (15, 75%).

[0172] In 20 patients with relapsed/refractory NPMl-m AML (median 3 prior lines) treated with ziftomenib 600 mg daily across Phase la and Phase lb, the complete remission (CR) rate at the cutoff date was 35% (95% confidence interval [CI], 15.4-59.2) with a composite remission (CR/CRh) rate of 40% and an overall response rate (ORR) of 45% (95% CI, 23.1-68.5). CR/CRh responses were durable (5.6 months; 7.7 months for CRc responders) and were associated with marrow blast reduction, count recovery, transfusion independence, and negative testing for measurable residual disease (MRD). Median overall survival for the 20 NPMl-m patients treated with 600 mg was 5.6 months, and 12.1 months for CR/CRh responders.

[0173] A known menin resistance mutation, MEN1-M327I, was detected in 1 of 29 (3.4%) treated patients, who were tested by RNA next-generation sequencing of sequential marrow aspirates. No additional resistance mutations were detected, even among patients who had received at least two cycles of ziftomenib treatment and continued to have measurable leukemic burden, indicating that disease progression in these patients was not due to MEN1 mutations. In contrast, 39% (12 or 31) of patients treated with revumenib for at least 2 cycles were found to have one or more MEN1 mutations, often concurrent with clinical progression (Pemer et al., MEN1 mutations mediate clinical resistance to menin inhibition, Nature 2023, 615, 913-919).

[0174] Across all NPMl-m patients in Phase la and Phase lb, median time to response was 51 days (range, 26-225). The median duration of remission for all patients with NPMl-m across Phase la and Phase lb who achieved a composite CR was 7.7 months, with a median duration of follow-up of 13.4 months. One patient with a CR at the 200 mg dose had ongoing remission lasting 35 cycles. Two patients (1 CR and 1 CRh) proceeded to stem cell transplant and remained in remission as of the cutoff date, with one patient remaining on post-transplant ziftomenib maintenance. The 200 mg dose produced a lower (6.7%) CR/CRh recovery rate and a lower overall response rate of 13.3%, compared to the 600 mg dose.

[0175] QTc prolongation attributable to ziftomenib was not detected in this patient population. No significant drug-drug interactions were noted, as compared to 53% rate of QT prolongation observed as a treatment-related adverse event in patients treated with the menin inhibitor, revumenib (Issa et al., The menin inhibitor revumenib in KMT2A-rearranged or NPM1 -mutant leukaemia, Nature 2023, 615, 920-924). Cases of Grade 3 or higher differentiation syndrome were rare and were managed effectively. In patients treated with 200 mg or 600 mg ziftomenib, the rate of differentiation syndrome was lower in NPMl-m patients (15%) than in KMT2A-r patients (41%). Clinically significant cytopenias were not seen in patients achieving CR or CRh on study.

[0176] Tabulated data are shown in Tables 13 and 14.

Table 13. ^a CRc includes CR, CRh, CRi (including CRp), and MLFS; ^b Overall response rate includes CRc, MLFS; ^c Transfusion independence is defined as at least 56 consecutive transfusion free days post baseline. Baseline period is defined as +/- 28 days period from 1 ^st dose.

AML, acute myeloid leukemia; CB, clinical benefit; CI, confidence interval; CR, complete remission, CRc, composite complete remission (CR, CRh + CRi); CRh, complete remission with partial hematologic recovery; CRi, complete remission with incomplete hematological recovery; CRp, complete remission with incomplete platelet recovery; HSCT, hematopoietic stem cell transplantation; KMT2Ar, lysine [k] -specific methyltransferase 2- rearranged; MLFS, morphologic leukemia-free state; MRD, measurable residual disease; n, number; neg, negative; NE, not-evaluable; NPM1 -mutant, nucleophosmin 1; OS, overall survival; PD, progressive disease; RBC, red blood cell; SD, stable disease.

Table 14.

G. Summary

[0177] In summary, ziftomenib demonstrated safety and tolerability. Reported adverse events most often were consistent with features and manifestations of underlying disease. No evidence was observed of drug-induced QTc prolongation. Differentiation syndrome, an on-target effect, was managed with monitoring and/or intervention mitigations. Clinical activity of ziftomenib monotherapy was found to be optimal at the 600 mg dose. A favorable NPM1-m benefit/risk balance was achieved with pronounced activity and a 30% CR rate (n=20), which increased to 35% as the trial progressed, a 35% CR/CRh rate, which increased to 40% as the trial progressed, and an ORR of 40%, which increased to 45% as the trial progressed. High levels of ziftomenib tissue penetration may drive clearance of extramedullary disease in AML patients. Increased exposure beyond 600 mg dosing was not significantly correlated with an increased probability of clinical response for any genetic subgroup, and for NPM1-m subjects, in particular, an increase in exposure was not correlated with greater risk of > Grade 3 AEs (i.e., no increased safety risk with increasing exposure). Although earlier cuts of data focused on 200 mg dosing, the extended data set coupled with pharmacokinetic analyses show the superiority of the 600 mg dose over the 200 mg dose in providing peak exposure without a significantly increased risk of > Grade 3 adverse events. For the NPM1-m patient population, in particular, the 600 mg QD dose compares favorably to the 200 mg dose.

[0178] The 600 mg, once-daily dose was identified as the optimal biological dose and was approved by FDA as the recommended Phase 2 dose of ziftomenib for further studies in the NPM1-m AML population.

[0179] Although both NPM1-m and KMT2A-r AML are menin-dependent, it could be hypothesized that the same dosing regimen would be the optimal safe and effective dose for both groups. Indeed, although efficacy data generated in the combined population was encouraging, the safety profile differentiated the response rates and benefit-risk for the two genotypes, likely due to more extensive extramedullary disease in the KMT2A-r subtype.

[0180] In Phase la, there was a significant overlap in exposure between the 200 mg and 400 mg dose levels and between the 400 mg and 600 mg dose levels, suggesting that clinical efficacy would be similar across all dose levels. Nevertheless, a clinically meaningful difference in response rates in NPM1-m patients across the combined Phase la/lb study was observed, with a 16.7% CR rate at 200 mg and a rapid and durable 35% CR rate at 600 mg. The treatment effect associated with CR includes rapid recovery of hematologic parameters contributing to transfusion independence.

[0181] The safety profile for ziftomenib for both genotypes combined is impacted by the experience of KMT2A-r patients and is differentiated from that observed in NPM1-m patients. With respect to differentiation syndrome, in particular, no fatal or life-threatening cases of DS were reported in NPM1-m patients, and all cases in this population were tolerable, reversible, and generally low-grade. In addition, instances of DS in NPM1-m patients were associated with clinical response and occurred in three of four NPM1-m patients experiencing DS. The severity of DS among KMT2A-r patients may relate to extensive extramedullary disease specific to disease of this genotype.

H. Resistance Mutation Studies

[0182] Various somatic resistance mutations in MEN1 have been reported following menin inhibitor therapy, including MEN1-M327I, MEN1-T349M, MEN1-G331R, and MEN1-G331D. For example, the T349 mutation was detected in a majority of patients who acquired menin gatekeeper mutations in another recent menin inhibitor clinical trial (Perner, F., Stein, E.M., Wenge, D.V. et al. MEN1 mutations mediate clinical resistance to menin inhibition. Nature 615, 913-919 (2023)). In the ziftomenib Phase 1 trial described herein, mutational analysis (RNAseq) of clinical samples following treatment with ziftomenib revealed that one resistance mutation, MEN1-M327I, developed in 1 of 29 patients tested (3.4%). In the one patient, the mutation was detected at C4D28, but the patient maintained stable disease through Cycle 7. It has been reported that while ziftomenib binding to M327I-mutant MEN1 in a menin-MLL binding assay was reduced relative to binding to wild-type protein, ziftomenib retained sub- 100 nM IC50 binding activity against the T349M variant. Data are shown in Table 15 (Grembecka, Development of new targeted therapeutics for AML, Presentation at 3 ^rd Biennial Miami Leukemia Symposium, March 31 -April 2, 2023).

Table 15.

[0183] In summary, from the data obtained to date, resistance mutations appear to develop infrequently following treatment with ziftomenib, and ziftomenib retains binding activity against a common menin gatekeeper mutation that has been observed in response to exposure to a menin inhibitor.

[0184] Thus, provided herein is a method of inhibiting the MEN1-MLL interaction comprising contacting MEN1 with ziftomenib, wherein the MEN1 comprises a resistance mutation, wherein the resistance mutation is optionally selected from mutations at M327, T349, S160, and G331, and combinations thereof, optionally wherein the mutation is selected from M327I, M327V, T349M, S160T, G331R, and G331D, and combinations thereof. In addition, in some embodiments of the methods provided herein, the acute leukemia, leukemia cell, or AML comprise MEN1 that comprises a resistance mutation, optionally wherein the resistance mutation is optionally selected from mutations at M327, T349, S160, and G331, and combinations thereof, optionally wherein the mutation is selected from M327I, M327V, T349M, S160T, G331R, and G33 ID, and combinations thereof. In some embodiments, the mutation is T349M or G33 ID. In some embodiments, the MEN1 resistance mutation is a de novo mutation. In some embodiments, the MEN1 resistance mutation is an acquired mutation, for example, that develops following exposure to a menin inhibitor.

[0185] While some embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. It is not intended that the invention be limited by the specific examples provided within the specification. While the invention has been described with reference to the aforementioned specification, the descriptions and illustrations of the embodiments herein are not meant to be construed in a limiting sense. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. Furthermore, it shall be understood that all aspects of the invention are not limited to the specific depictions, configurations, or relative proportions set forth herein which depend upon a variety of conditions and variables. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is therefore contemplated that the invention shall also cover any such alternatives, modifications, variations, or equivalents. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.