Methods of treating acute leukemia

Abstract

Provided herein are methods of treating acute leukemia, such as acute myelogenous leukemia (AML), in an individual, such as an individual having a mutation in the nucleophosprotein 1 (NPM1) gene or a rearrangement in the lysine [K]-methyltransferase 2A (KMT2A) gene, wherein the method comprises administering to the individual the menin inhibitor zitomenib at a dose of 600 mg per day.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] 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 Art

[0003] 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 lymphoblastic leukemia (ALL). AML is a highly lethal group of blood cancers and is characterized by the proliferation of myeloid precursors (myeloid blasts or promyelocytes) and their inability to undergo normal differentiation. AML is caused by a series of genetic changes in hematopoietic precursor cells. These changes alter normal hematopoietic growth and differentiation, leading to the abnormal accumulation of large numbers of these immature myeloid blasts in the bone marrow and peripheral blood, thereby interfering with the production of normal blood cells. Similar to other malignancies, the genetic changes in AML include mutations in oncogenes and deletions in tumor suppressor genes. However, unlike most solid tumors, many hematological malignancies are associated with a single characteristic cytogenetic abnormality. This clinically heterogeneous disease is characterized by multiple chromosomal abnormalities and gene mutations, which lead to significant differences in response to chemotherapy and survival, and also pose a major challenge to successful and long-lasting AML treatment. (Kumar, CC, Genes Cancer 2011, 2(2), 95-107.) Similarly, ALL involves genetic changes that lead to the production of leukemic lymphoblasts in the bone marrow, which in turn affect the 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 cancer death in children. Although most ALL cases occur in children, 80% of ALL deaths occur in adults. Summary of the Invention

[0004] Provided herein are methods of treating an acute leukemia (such as acute myeloid leukemia (AML) or acute lymphoblastic leukemia (ALL)) in a subject, or methods of inhibiting proliferation of leukemic cells in a subject and / or inducing apoptosis in leukemic cells, wherein the acute leukemia or leukemic cells comprise 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 600 mg of ziftomenib or an isotopologue thereof, or a pharmaceutically acceptable salt or 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, to the subject daily. In some aspects, the acute leukemia is menin-dependent. In some aspects, the acute leukemia or leukemic cells comprise 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, zitomenib, administered at 600 mg daily, exhibits significant clinical efficacy in acute leukemia, as demonstrated by clinical response rates, coupled with a manageable safety and tolerability profile, particularly when administered to individuals with specific genetic abnormalities, including NPM1 mutations or KMT2A rearrangements. Also provided and described herein are methods of treating an acute leukemia (such as AML or ALL) in an individual, or methods of inhibiting proliferation of leukemia cells and / or inducing apoptosis in leukemia cells 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 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, comprising administering 600 mg of zitomenib, or a pharmaceutically acceptable form thereof, or a pharmaceutical composition comprising zitomenib, or a pharmaceutically acceptable form thereof, daily 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.

[0005] Provided herein are methods for treating extramedullary leukemia in an individual with acute leukemia, comprising administering to the individual a therapeutically effective amount of a menin inhibitor, particularly 600 mg of zitomenib daily or a pharmaceutically acceptable form thereof, 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 aggregates of leukemic cells outside the medullary cavity of the bone marrow, optionally in the form of a myeloblastic solid tumor. In some aspects, the extramedullary leukemia is menin-dependent. Also provided herein is a method for treating extramedullary leukemia in an acute leukemia individual, 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, 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, comprising administering 600 mg of zitomenib or a pharmaceutically acceptable form thereof to the individual daily, or a pharmaceutical composition comprising zitomenib or a pharmaceutically acceptable form thereof. In some aspects, the extramedullary leukemia comprises an NPM1 mutation, optionally combined 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. In some aspects, the acute leukemia is AML or ALL.

[0006] Also provided herein is a method for increasing the level of myeloid blasts in the blood of an AML individual, comprising administering to the individual a therapeutically effective amount of a menin inhibitor, particularly 600 mg of zitomenib daily or a pharmaceutically acceptable form thereof, wherein the AML optionally comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation. It has been observed that zitomenib causes a significant and stable increase in the level of blasts in the blood, a condition that generally indicates leukemia disease progression. However, for zitomenib, it has been found that the release of blasts from the bone marrow into the intramedullary space is associated with the sensitivity of the leukemia to zitomenib therapy, and in this case, this effect does not indicate 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 level of myeloid blasts can be temporary, and the myeloid blasts in the blood can subsequently decrease.

[0007] Also provided herein is a method of identifying an individual whose acute leukemia is susceptible to administration of a menin inhibitor, particularly zitomenib, comprising:

[0008] administering to the individual an effective amount of the menin inhibitor, particularly 600 mg of zitomenib or a pharmaceutically acceptable form thereof per day;

[0009] obtaining, at a first time point before the start of the administering or during the administering, an identification result of the level of myeloid blasts in a first blood sample collected from the individual;

[0010] obtaining an identification of the level of myeloid blasts in a second blood sample collected from the individual at a second time point after the first time point and during the administration; and

[0011] determining that the acute leukemia is sensitive to the administration if the level of myeloid blasts at the second time point is higher than the level at the first time point;

[0012] 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 wherein the acute leukemia comprises an NPM1 mutation or a KMT2A rearrangement.

[0013] 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.

[0014] Also provided herein are methods of treating a differentiation disorder in an individual diagnosed with a differentiation disorder and an acute leukemia, or methods of reducing the risk of an individual with an acute leukemia developing a severe differentiation disorder, 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 wherein the acute leukemia comprises an NPM1 mutation or a KMT2A rearrangement comprising:

[0015] (a) administering to the individual a therapeutically effective amount of a menin inhibitor, in particular 600 mg per day of zitomenib or a pharmaceutically acceptable form thereof;

[0016] (b) administering IV rehydration to the individual, and optionally,

[0017] (c) administering to the individual an effective amount of a xanthine oxidase inhibitor, optionally wherein the xanthine oxidase inhibitor is allopurinol, optionally at a dose of about 200-400 mg / m 2The allopurinol is administered in 1-3 divided doses per day, up to a maximum of about 800 mg per day. 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.

[0018] Also provided herein are methods of treating a differentiation disorder in an individual with acute leukemia or reducing the risk of an individual with acute leukemia developing a severe differentiation disorder, 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:

[0019] (a) administering to the individual an effective amount of a menin inhibitor, in particular 600 mg of zitomenib or a pharmaceutically acceptable form thereof per day;

[0020] (b) administering IV rehydration to the individual, and

[0021] (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.

[0022] 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.

[0023] The present invention also provides a method for treating a differentiation disorder in an individual with acute leukemia or reducing the risk of developing a severe differentiation disorder, optionally wherein the acute leukemia is a menin-dependent leukemia, 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:

[0024] (a) administering to the individual a prophylactic and / or effective amount of a corticosteroid, 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

[0025] (b) administering to the individual a therapeutically effective amount of a menin inhibitor.

[0026] 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.

[0027] 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 600 mg of zitomenib, or a pharmaceutically acceptable form thereof, or a pharmaceutical composition comprising zitomenib, or a pharmaceutically acceptable form thereof, daily to the individual.

[0028] Also provided herein is a pharmaceutical composition comprising an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or a submaximal tolerated dose of zitomenib, 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 submaximal tolerated dose is 600 mg. In some embodiments, zitomenib, or a pharmaceutically acceptable form thereof, has Breakthrough Therapy designation.

[0029] Incorporation by reference

[0030] 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

[0031] Figure 1 : Trough concentrations of zitomenib in plasma (ng / mL) or in bone marrow, heart, or spleen tissue (ng / g) after daily dosing.

[0032] Figure 2 : Mean change from baseline in peripheral blasts (orange) and leukocytes (blue) at (a) cycle 1, day 8; (b) cycle 1, day 15; and (c) cycle 2, day 1.

[0033] Figure 3A-3C : After daily administration of 50, 200, 400, 600 and 800 mg of zitomenib, the AUC at steady state was 0-24 、C 谷值 and C 最大值 Determine the exposure level. Figure 3A : AUC at steady state 0-24 . Figure 3B : C in steady state 谷值 level. Figure 3C : C in steady state 最大值 level.

[0034] Figure 4A-4B : Relationship between MEIS1 expression and dosage in different genetic subtypes. Figure 4A : Individual object data. Figure 4B : Average expression level. DETAILED DESCRIPTION

[0035] Epigenetic modification of the lysine methyltransferase 2A (KMT2A) gene causes KMT2A to fuse with more than 60 partner genes and plays a pathogenic role in the onset, development, and progression of a subset of acute leukemias (Borkin et al., Cancer Cell 2015, 27(4), 589-602). HOXA9 and MEIS1 are key oncogenes overexpressed in KMT2A rearranged leukemias. (Thiel et al., Bioessays 2012, 34(9), 771-780.) HOXA9 and MEIS1 transcription factors drive AML by upregulating stem cell programs and hindering myeloid differentiation. KMT2A (MLL) rearrangement alters the normal histone methyltransferase function of KMT2A (MLL) and dysregulates these HOX genes, leading to persistently high HOX levels and hindering hematopoietic (myeloid) differentiation, ultimately leading to acute leukemia. (Kühn 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.) Translocation (rearrangement) in the KMT2A gene (KMT2A-r) occurs in 5-10% of AML patients, and the 5-year survival rate of KMT2A-r patients is less than 20% (Issa, 2021).

[0036] Nucleoplasmin 1 (NPM1) encodes a protein involved in the transport of cellular proteins to the nucleolus. NPM1 also drives the expression of leukemia-causing genes through its interaction with menin and wild-type KMT2A (MLL) (Kühn, 2016). The NPM1 gene is upregulated, mutated, and undergoes chromosomal translocations in many tumor types.

[0037] In AML, a key common factor in KMT2A (MLL) regulation of these leukemic genes is the interaction between the N-terminal portion of KMT2A (MLL) and menin, which is crucial for directing the gene activation effects of both wild-type KMT2A (MLL) and KMT2A (MLL) fusion proteins to the promoter regions of HOXA9 and MEIS1. Menin is a highly specific and direct binding partner of KMT2A (MLL) and KMT2A (MLL) fusion proteins and is required for the regulation of their target genes (Yokoyama et al., Cell 2005, 123 (2), 207-218.). Numerous studies have demonstrated that menin plays a key role as an oncogene cofactor in leukemic transformation mediated by KMT2A (MLL) fusion proteins, and recently, menin has also been shown to drive overexpression of HOXA9 and MEIS1 in a subset of normal karyotype AML 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 (regardless of whether they have other mutations), and the 5-year survival rate of AML patients with NPM1 mutations (NPM1-m) is approximately 50% (Angenendt et al., J. Clin. Oncol. 2019, 37(29), 2632-2642; Thiede et al., Blood 2006, 107(10), 4011-4020).

[0038] Other genetic modifications that negatively impact disease progression and prognosis include mutations in another histone methyltransferase gene called SET domain-containing 2 (SETD2), including truncating mutations, which are found in 1-2% of AML cases; and mutations in the gene encoding runt-related transcription factor 1, also known as acute myeloid leukemia 1 protein (RUNX1), a transcription factor that regulates the differentiation of hematopoietic stem cells into mature blood cells. Chromosomal translocations involving RUNX1 have been associated with multiple types of leukemia, including AML.

[0039] The standard of care treatment for AML and ALL is intensive chemotherapy (a combination of anthracyclines (e.g., daunorubicin or idarubicin) and cytarabine in the "7+3" regimen), which has been used for more than 40 years. However, intensive chemotherapy has a series of difficult side effects and is not suitable for patients with poor health (such as elderly patients), and the outcome of standard chemotherapy remains unsatisfactory. In addition, even if patients respond, more than half of adult patients and about 80% of elderly patients will develop primary refractory disease, relapse, or treatment-related death. Although improvements in supportive care have improved overall survival (OS), up to 30%-40% of patients will develop refractory disease (i.e., failure to achieve a morphological complete response (CR) after one to two cycles of induction therapy), and the median survival of these patients is less than one year. (Horibata et al., Proc. Natl. Acad. Sci. 2019, 116(21), 10494-10503.) Patients can also be treated with stem cell transplantation.

[0040] AML accounts for approximately 30% of all adult leukemia cases and 80% of all adult acute leukemia cases. The outcome for AML patients is generally considered dire or poor, with the outcome further characterized by a high mortality rate. In particular, the presence of NPM1-m is associated with a risk of refractoryness 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 leads to a group of aggressive and poorly prognostic 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-rAML.

[0041] Zitomenib (KO-539) is a potent and selective inhibitor of the menin-KMT2A (MLL) complex, with downstream effects on HOXA9 / MEIS1 expression. (Burrows et al., Proceedings of the AACR EORTC International Conference: Molecular Targets and Cancer Therapeutics; October 26-30, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Mol. Cancer Ther. 2018; 17(1 Suppl): Abstract No. LB-A27.) KOMET-001 (NCT04067336) is a Phase 1 / 2, open-label study evaluating zitomenib in adult patients with relapsed and / or refractory AML, including those with select NPM1 mutations or KMT2A rearrangements, both of which represent particularly aggressive forms of this blood cancer for which there is a high unmet need, particularly once the disease has relapsed or become refractory to existing therapies. (See https: / / kuraoncology.com / clinical-trials / clinical-trials-komet-001 / , accessed in October 2023.) This study examined the safety and tolerability, pharmacokinetics, and antitumor activity of zitomenib in these AML groups. The study endpoints also included determining the optimal biologic dose or recommended phase 2 dose.

[0042] Provided herein are methods for treating acute leukemias, such as AML or ALL, particularly AML, wherein the methods in some aspects comprise administering zitomenib to an individual at a daily dose of 600 mg. The methods provided herein generally encompass the following findings: individuals with acute leukemias (e.g., AML or ALL, particularly AML) exhibit increased response rates and / or improved safety profiles when treated with zitomenib, 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-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, particularly comprising a mutation in the NPM1 gene. For example, treatment of NPM1-m AML comprising administering 600 mg of the menin inhibitor zitomenib is more effective and produces a better safety profile than treatment of non-NPM1-m AML at the same dose. Thus, 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 zitomenib, 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.

[0043] In addition, in some embodiments, zitomenib or a pharmaceutically acceptable form thereof is provided for use in a method of treating an 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 is the use of zitomenib or a pharmaceutically acceptable form thereof in a method of treating AML with an NPM1 mutation. Similarly, in some embodiments, zitomenib or a pharmaceutically acceptable form thereof is provided for treating an individual's acute leukemia (e.g., AML or ALL, particularly AML), 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, particularly 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.

[0044] Zitomenid and its pharmaceutically acceptable forms

[0045] Zitomenid is a potent inhibitor of menin-MLL (KMT2A) interaction (IC 50 22 nM) and selective inhibitors are in clinical development for the treatment of acute leukemias, including NPM1-mutated (NPM1-m) and KMT2A-rearranged (KMT2A-r) AML, as well as other genetically defined acute leukemia subgroups with high unmet needs.

[0046] Zitomenil is a compound with the following structure:

[0047]

[0048] Alternatively designated as (S)-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 utilize a pharmaceutically acceptable form of zitomenib. In some embodiments, the methods described herein utilize zitomenib or a pharmaceutically acceptable salt thereof. In some embodiments, the methods described herein utilize zitomenib or a solvate thereof. In certain embodiments, zitomenib comprises the free base form or a solvate thereof. In some embodiments, stereoisomers and / or metabolites of zitomenib are also encompassed.

[0049] In some embodiments, the menin inhibitor described herein is zitomenib or a pharmaceutically acceptable form thereof.

[0050] Zitomenid dosage and administration schedule

[0051] In some embodiments, the methods provided herein comprise administering an effective amount (such as 600 mg) of zitomenib or a pharmaceutically acceptable form thereof to an individual daily. In some embodiments, the method comprises administering to an individual daily an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or zitomenib or a pharmaceutically acceptable form thereof that is lower than the maximum tolerated dose. 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 lower than the maximum tolerated dose is 600 mg. In some embodiments, a 600 mg dose is a safe and effective amount. In some embodiments, zitomenib or a pharmaceutically acceptable form thereof has breakthrough therapy designation.

[0052] In some embodiments, administering zitomenib or a pharmaceutically acceptable form thereof comprises administering to the individual at least 3 days, or at least 5 days, or at least 7 days, or at least 10 days, or at least 14 days, or at least 21 days, or at least 28 days, or for a period of at least 28 days, or for a period of 28 days.

[0053] In certain embodiments, zitomenib, or a pharmaceutically acceptable form thereof, is administered to an individual daily for a period of at least 28 days, or for a period of 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., there are 0 days between cycles).

[0054] In certain embodiments, zitomenib or a pharmaceutically acceptable form thereof is administered orally.

[0055] In some embodiments, daily administration is administration once or twice daily. In some embodiments, daily administration is once daily.

[0056] The amount of zitomenib dose referred to herein refers to the free base amount (if the free form is used) or the free base equivalent amount (if a salt and / or solvate is used). Thus, for example, if a salt form is used, the total mass of the daily dose will exceed 600 mg, but the total mass will be selected to provide 600 mg of zitomenib free base equivalent.

[0057] In some embodiments, zitomenib, or a pharmaceutically acceptable form thereof, is administered in combination with a P-gp inhibitor or a breast cancer resistance protein (BCRP) inhibitor.

[0058] Pharmaceutical composition

[0059] Also provided herein is a pharmaceutical composition comprising an optimal biological dose, recommended Phase 2 dose, safe and effective dose, or submaximal tolerated dose of zitomenib, or a pharmaceutically acceptable form thereof. In some embodiments, the optimal biological dose, recommended Phase 2 dose, safe and effective dose, or submaximal tolerated dose is 600 mg. In some embodiments, zitomenib, or a pharmaceutically acceptable form thereof, has 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 50 to 600 mg of zitomenib, or comprises 50 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg, or 600 mg of zitomenib. In some embodiments, the total amount of zitomenib 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 zitomenib. In some embodiments, each oral dosage form comprises 200 mg or 300 mg of zitomenib. In some embodiments, zitomenib administered in the methods provided herein is administered using such pharmaceutical compositions or oral dosage forms.

[0060] AML and ALL

[0061] In some embodiments, provided herein are methods for treating acute myeloid leukemia (AML).AML is a bone marrow disease and hematopoietic stem cell disorder characterized by genetic changes in blood cell precursors leading to excessive production of tumorous clonal myeloid stem cells. Although extramedullary manifestations (such as myeloid sarcoma, skin leukemia) may occur, underlying diseases are generally caused by abnormal production of blood cells. In certain embodiments, acute myeloid leukemia (AML) includes 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 care), which includes cytarabine and anthracycline (idarubicin or daunorubicin), typically using a 7+3 combination, i.e., continuous infusion of cytarabine and intermittent administration of anthracycline, administered within 7 days and within 3 days, respectively. In certain embodiments, for newly diagnosed AML patients who do not meet the 7+3 program qualifications or unit requirements, first-line standard care is venetoclax plus azacitidine (ven / aza). In some embodiments, the AML is resistant to ven or ven / aza. In some embodiments, the AML progresses during 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 megakaryocytic leukemia.

[0062] In some embodiments, the methods provided herein are directed to treating acute lymphoblastic leukemia (ALL). ALL is a type of blood and bone marrow cancer that involves the uncontrolled proliferation of abnormal, immature lymphocytes, leading to bone marrow replacement and blood invasion. In certain embodiments, ALL includes relapsed ALL, refractory ALL, or both relapsed and refractory ALL. In certain embodiments, ALL is refractory ALL. In some embodiments, ALL is relapsed ALL. In some embodiments, ALL is both refractory and relapsed ALL. In some embodiments, ALL is precursor B acute lymphoblastic leukemia, precursor T acute lymphoblastic leukemia, Burkitt's leukemia, or acute biphenotypic leukemia.

[0063] Genetic alterations in acute leukemia

[0064] In some embodiments, the acute leukemia or leukemia cell is characterized by (e.g., one or more) genetic alterations, which can be selected from NPM1 mutations, KMT2A rearrangements, SETD2 mutations, and RUNX1 mutations. 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-PTD. In some embodiments, the acute leukemia or leukemia cell comprises a 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 a SETD2 mutation and a RUNX1 mutation. In some embodiments, the acute leukemia or leukemia cell comprises one or more mutations selected from FLT3, FLT3-ITD, FLT3-TKD, IDH, IDH1, IDH2, TERT, and BRAF. In some embodiments, acute leukemia or leukemia cells include NPM1 mutations, KMT2A rearrangements, KMT2A-PTD mutations, SETD2 mutations, RUNX1 mutations, FLT3-ITD mutations, FLT3-TKD mutations, IDH mutations (such as IDH1 mutations or IDH2 mutations), TERT mutations or BRAF mutations, or any combination thereof. In some embodiments, acute leukemia or leukemia cells include NPM1 mutations, and optionally include one or more mutations selected from FLT3 (such as FLT3-ITD or FLT3-TKD), IDH (such as IDH1 mutations or IDH2 mutations), TERT or BRAF. In some aspects, acute leukemia includes NPM1 mutations, optionally combined with FLT3 mutations (such as FLT3 internal tandem duplication (ITD) mutations or FLT3 mutations in tyrosine kinase domains (FLT3-TKD mutations)) or IDH mutations (such as IDH1 mutations or IDH2 mutations) or combinations thereof.

[0065] In certain embodiments, the mutated NPM1 gene comprises one or more mutations relative to the wild-type NPM1 gene sequence. NPM1 generally refers to and encompasses the gene encoding the NPM1 protein (e.g., see UniProt ID P06748). In some cases, the NPM1 gene comprises NCBI gene ID 4869 and / or NCBI reference sequence: NG_016018.1 (5001..28181). NPM1 mutations are present in approximately 25%-30% of AML cases, and in some cases, are typically characterized by the presence of a typical 4-base pair insertion, which generates a new N-terminal nuclear export signal, leading to abnormal cytoplasmic accumulation of the mutant NPM1c protein. NPM1 mutations include type A, type B, and type D mutations, which are characterized by a 4-nucleotide insertion in exon 12, resulting in cytoplasmic localization of NPM1 (NPM1-c). In certain circumstances, NPM1-c binds to and mislocalizes transcription factors that normally promote myeloid lineage differentiation but can also be re-imported into the nucleus by XPO1 and directly influence gene expression.

[0066] 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, the NPM1 mutation comprises a type C mutation. In certain embodiments, the NPM1 mutation comprises a type D mutation. In certain embodiments, the 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 the NPM1 gene.

[0067] 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. Translocations (9;11)(p22;q23)(MLLT3;KMT2A) or t(10;11)(p12;q23)(AF10;KMT2A) have been reported in 4% of adult myeloid leukemias. Similarly, multiple SETD2 and RUNX1 mutations have been reported in association with acute leukemia.

[0068] In some embodiments, acute leukemia or leukemia cells comprise more than one mutation or rearrangement. In some embodiments, acute leukemia or leukemia cells comprise (a) NPM1 mutation or KMT2A rearrangement, and (b) at least one mutation selected from FLT3 (such as FLT3-ITD or FLT3-TKD), IDH (eg, IDH1 or IDH2), TERT, and BRAF. In some embodiments, acute leukemia or leukemia cells comprise (a) NPM1 mutation, and (b) at least one mutation selected from FLT3 mutation (such as FLT3-ITD or FLT3-TKD) or IDH (such as IDH1 or IDH2).

[0069] In some cases, characterization of a genetic mutation or rearrangement can be achieved by collecting a bone marrow (BM aspirate), whole blood sample, and / or tumor sample and then performing known assays for nucleic acid analysis. In certain embodiments, the mutation or rearrangement is detected by sequencing (e.g., genomic sequencing), such as by CLIA-validated next generation sequencing assays for mutations in 194 genes associated with AML. In certain embodiments, specific mutations or rearrangements are detected by molecular testing, such as by polymerase chain reaction (e.g., followed by fragment analysis and / or capillary gel electrophoresis). In certain embodiments, mutations or rearrangements are detected by RT-PCR or quantitative PCR. In some embodiments, the methods provided herein include detecting mutations or rearrangements or obtaining identification of mutations or rearrangements, particularly NPM1 mutations, prior to administering zitomenib, optionally wherein the NPM1 mutation is assayed by next generation sequencing or PCR.

[0070] Efficacy

[0071] As described in Example 3, efficacy outcomes of patients treated with zitomenib were evaluated according to CR rate, CR / CRh rate, and CRc rate, as well as 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 about 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, or 35%, or about 35%. In some embodiments, the CR rate is at least about 35%, or 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 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 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%.

[0072] In some embodiments, patients with a particular genetic profile have a higher CR rate, CR / CRh rate, CRc rate, and / or ORR rate. In some embodiments, patients with acute leukemia (such as AML) with an NPM1 mutation have a higher CR rate, CR / CRh rate, CRc rate, and / or ORR rate than patients without an NPM1 mutation.

[0073] In some embodiments, the duration of remission (DoR) for patients achieving CRc (such as NPM1-m AML patients) 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 NPM1-m patients achieving CRc is at least about 8 months, or at least about 8.2 months, or about 8.2 months. In some embodiments, the DoR for NPM1-m patients achieving CRc is at least about 5 months, or at least about 6 months, or at least about 7 months, or about 5.6 months, or about 6.6 months, or about 7.7 months. In some embodiments, the DoR for NPM1-m patients achieving CRc by administration of 600 mg of zitomenib is about 5 to 7 months, or about 5.6 months, or about 6.6 months. In some embodiments, the DoR for NPM1-m patients who achieve a 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 NPM1-m patients who achieve a CR or CRh by administration of 600 mg of zitomenib 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.

[0074] In some embodiments, the median overall survival (OS) is at least about 5 months, or about 5.1 months, or about 5.6 months, or at least 5 months, or at least 5.5 months. In some embodiments, NPM1-m patients treated with 600 mg of zitomenib achieved such an OS. In some embodiments, the OS of NPM1-m patients treated with 600 mg of zitomenib is longer than that of NPM1-m patients treated with 200 mg of zitomenib.

[0075] In some embodiments, administration results in a temporary increase in white blood cell count or peripheral blast count, followed by a decrease in that count. In some embodiments, the temporary increase occurs within 14 days after the start of treatment. In some embodiments, the decrease occurs within 14 days after the increase. In some embodiments, provided herein are methods for temporarily increasing white blood cell count or peripheral blast count, comprising administering an effective amount of zitomenib or a pharmaceutically acceptable form thereof, for example, 600 mg of zitomenib or a pharmaceutically acceptable form thereof. In some embodiments, the increase from baseline occurs within one week, two weeks, three weeks, or four weeks after the start of administration. In some embodiments, the increase from baseline persists for about one week, about two weeks, or about three weeks.

[0076] Security

[0077] In some embodiments, the methods provided herein comprise administering zitomenib or a pharmaceutically acceptable form thereof to an individual, wherein the risk of individuals of one genetic subtype exhibiting or developing a particular side effect (or serious side effect) is reduced relative to 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 of the side effect in a modified intention-to-treat (mITT) patient population (independent of dose), as results indicate that safety outcomes are not completely dose-related (see Example 3), or based on the incidence of the side effect in different genetic groups (e.g., NPM1-m group compared to KMT2A-r group).

[0078] In some embodiments, the methods disclosed herein include the following features: when the individual has an acute leukemia (e.g., AML or ALL), particularly AML, with an NPM1 mutation, the individual is at lower risk for developing certain adverse events than individuals without the NPM1 mutation. In some embodiments, individuals with an acute leukemia comprising an NPM1 mutation are at lower risk for 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 suspected adverse event of differentiation syndrome, differentiation syndrome, or severe differentiation syndrome than individuals with an acute leukemia that does not comprise an NPM1 mutation.

[0079] In some embodiments, the methods comprise administering zitomenib, or a pharmaceutically acceptable form thereof, wherein the risk of a subject administered zitomenib developing any Grade 3 or higher treatment-emergent adverse event (TEAE), regardless of causality, following administration is less than about 80%, or less than about 75%, or about 71%. In some embodiments, the methods comprise administering zitomenib, or a pharmaceutically acceptable form thereof, wherein the risk of a subject developing any serious adverse event, regardless of causality, following administration is less than about 65%, or less than about 60%, or less than about 55%, or about 53%.

[0080] In some embodiments, the method comprises administering zitomenib or a pharmaceutically acceptable form thereof, wherein the risk of the individual developing any suspected adverse event of differentiation syndrome after administration 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 about 47%. As used herein, a "suspected adverse event of differentiation syndrome" is differentiation syndrome, a treatment-emergent adverse event (TEAE) that meets Norsworthy criteria for possible differentiation syndrome, or a TEAE that meets Norsworthy criteria in which differentiation syndrome cannot be ruled out. (Norsworthy et al., Clin. Cancer Res. 2020, 26(16), 4280-4288.)

[0081] In some embodiments, the method comprises administering zitomenib or a pharmaceutically acceptable form thereof, wherein the risk of the individual developing differentiation syndrome following administration is less than about 25%, or less than about 20%, or less than about 19%, or less than about 18%, or about 18%. In some embodiments, the probability that the individual will develop grade 3, 4, or 5 severe differentiation syndrome is less than about 50%, or less than about 45%, or less than about 40%, or less than about 35%, or about 33%.

[0082] In some embodiments, the method comprises administering zitomenib 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 about 6%. As used herein, "severe differentiation syndrome" is defined as differentiation syndrome of grade 3, 4, or 5 according to the Common Toxicity Criteria for Adverse Events standardized by the National Cancer Institute (available at http: / / ctep.cancer.gov / protocolDevelopment / electronic_applications / ctc.htm).

[0083] In some embodiments, the method comprises administering zitomenib or a pharmaceutically acceptable form thereof, wherein the individual develops differentiation syndrome following administration, and the probability that the differentiation syndrome is not severe differentiation syndrome (e.g., 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 about 67%.

[0084] In some embodiments, the methods provided herein comprise administering zitomenib, or a pharmaceutically acceptable form thereof, without inducing QTc prolongation.

[0085] Differentiation disorders

[0086] Preclinical studies have found that zitomenib can drive terminal differentiation and programmed apoptosis. A potentially serious sequelae is differentiation syndrome (DS), which can be life-threatening or even fatal if not treated. Differentiation syndrome has been found in patients receiving isocitrate dehydrogenase (IDH) inhibitors (Norsworthy, 2020) and has also been reported in patients after administration of zitomenib, with fatal outcomes. Increasing recognition of DS signs and symptoms through the Montesinos framework can enable early diagnosis and treatment and reduce the rate 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 pleural pericardial effusions. Patients who meet two or three of the criteria are classified as having moderate DS, and patients who meet at least four criteria are classified as having severe DS.

[0087] As used herein, "differentiation disorder" refers to differentiation syndrome (with or without leukocytosis), leukocytosis, and tumor lysis syndrome. Leukocytosis can be detected based on an increase in white blood cell count in the absence of infection. Tumor lysis syndrome can occur in the setting of rapidly progressive leukocytosis and can be detected by the presence of two or more blood chemistry markers selected from hyperuricemia, hyperkalemia, hyperphosphatemia, and hypocalcemia, or by an increase in serum creatinine levels.

[0088] Monitor and assess the following adverse events in treated patients using an algorithm based on the Montesinos criteria (as described by Norsworthy (2020)), and apply the diagnostic criteria described below to patients who received at least one dose of zolpidem.

[0089] A differentiation disorder, such as DS, with or without leukocytosis, may be suspected based on one or more of the following symptoms:

[0090] New or worsening progressive dyspnea or hypoxia with increased need for supplemental oxygen and no clear alternative cause

[0091] Radiographic evidence of new or worsening pulmonary infiltrates that cannot be attributed to another cause;

[0092] Radiographic evidence of new or worsening pleural or pericardial effusion of unknown etiology or refractory to treatment of the initially suspected cause;

[0093] New or worsening peripheral edema of unknown etiology accompanied by rapid weight gain (e.g., >5 kg in 7 days);

[0094] Acute renal failure (e.g., serum creatinine increased >2-fold from baseline) not attributable to other causes or medications;

[0095] Unexplained fever ≥ 38°C (100.4°F);

[0096] Unexplained hypotension;

[0097] Significant changes in inflammatory markers;

[0098] Evidence of multiple organ dysfunction; or

[0099] Rash, joint pain, bone pain, or swelling in extramedullary lesions.

[0100] The presence of two or more of the above signs and symptoms can be considered potential DS. Patients who meet two or three of the criteria are classified as having moderate DS, and those who meet at least four criteria are classified as having severe DS.

[0101] Notably, it was found that the development of differentiation syndrome in AML patients with NPM1 mutations was associated with a good outcome. In some embodiments, the treated individual develops differentiation syndrome, optionally wherein the differentiation syndrome is severe differentiation syndrome (e.g., Grade 3, Grade 4, or Grade 5), but there is still a probability of achieving an ORR of at least about 60%, or at least about 65%, or at least about 70%, or at least about 75%, or about 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, or 75%.

[0102] It has also been found that treating patients with zitumenib or a pharmaceutically acceptable form thereof increases the level of myeloid blasts in the blood of treated individuals. Therefore, provided herein is a method for increasing the level of myeloid blasts in the blood of AML individuals, comprising administering an effective amount of a menin inhibitor to the individual, particularly 600 mg of zitumenib or a pharmaceutically acceptable form thereof daily, optionally wherein AML is menin-dependent, or optionally wherein 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 AML comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation. In some embodiments, AML comprises an NPM1 mutation or a KMT2A rearrangement. In some embodiments, AML comprises an NPM1 mutation. In some embodiments, the relative level of myeloid blasts in the blood of an individual is assessed by analyzing blood samples at two time intervals from the individual, optionally, wherein the blood samples are collected at, for example, (a) a first time point and a second time point, wherein both time points are during administration, or (b) a first time point before administration and a second time point during administration. In some embodiments, the first time point is before administration, for example, before cycle 1, day 1, and the second time point is at least 7, 14, 21 or 28 days later, or is from cycle 1, day 2 to cycle 1, day 28 on a certain day. In some embodiments, each analysis is a complete blood count (CBC), optionally with a differential count. In some embodiments, the first time point and the second time point are spaced 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 apart, or at intervals of a cycle (such as cycle 1) duration, or wherein the second time point is at the time when the individual reaches complete remission (CR). In some embodiments, the first time point is at screening, or at cycle 1, day 1. In some embodiments, an increase in the level of myeloid blasts in the individual's blood is not associated with the progression of 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 that the individual is sensitive to a menin inhibitor, particularly zitomenib or a pharmaceutical form thereof.

[0103] Monitoring and treatment of differentiation disorders

[0104] Monitoring and early intervention were found to reduce the occurrence and severity of differentiation disorders, allowing for a reduction in adverse events and enabling patients to continue treatment.

[0105] In some embodiments, the methods provided herein comprise administering an effective amount of a steroid (eg, dexamethasone) if a differentiation disorder is detected in the individual during administration of zitomenib or a pharmaceutically acceptable form thereof.

[0106] Provided herein are methods for identifying an individual whose acute leukemia (particularly AML) is sensitive to administration of a menin inhibitor (particularly zitomenib), comprising:

[0107] administering to the individual an effective amount of a menin inhibitor, particularly 600 mg of zitomenib or a pharmaceutically acceptable form thereof daily;

[0108] obtaining, at a first time point before the start of administration or during administration, an identification of the level of myeloid blasts in a first blood sample collected from the individual;

[0109] obtaining an identification of the level of myeloid blasts in a second blood sample collected from the individual at a second time point after the first time point and during the administration; and

[0110] If the level of myeloid blasts at the second time point is higher than the level at the first time point, the acute leukemia is determined to be sensitive to the administration;

[0111] Optionally, the acute leukemia is menin-dependent, or optionally, 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 optionally, 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.

[0112] 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.

[0113] In some embodiments, a method of treating a differentiation disorder, particularly tumor lysis syndrome, in an individual who is an acute leukemia individual diagnosed with a differentiation disorder, or a method of reducing the risk of an acute leukemia individual developing a severe differentiation disorder, 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 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 to the individual an effective amount of a menin inhibitor, particularly 600 mg daily of zitomenib or a pharmaceutically acceptable form thereof;

[0114] (b) administering IV rehydration to the individual, and optionally,

[0115] (c) administering to the individual an effective amount of a xanthine oxidase inhibitor, optionally wherein the xanthine oxidase inhibitor is allopurinol, optionally at a dose of about 200-400 mg / m 2 Allopurinol is administered in 1-3 divided doses per day, up to a maximum of about 800 mg per day.

[0116] 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.

[0117] Some embodiments comprise administering a xanthine oxidase inhibitor, and prior to administering the xanthine oxidase inhibitor, diagnosing the individual as having a low risk or an intermediate risk of having or developing a differentiation disorder by obtaining the individual's identification of:

[0118] (1) White blood cell count is less than about 25×10 9 / L and the lactate dehydrogenase level is less than twice the upper limit of normal (e.g., where the normal level is about 280 units / L), or

[0119] (2) White blood cell count is about 25 to about 100×10 9 / L, or

[0120] (3) White blood cell count is less than about 25×10 9 / L, and lactate dehydrogenase level is more than twice the upper limit of normal.

[0121] Provided herein are methods of treating a differentiation disorder in an individual with acute leukemia or reducing the risk of an individual with acute leukemia developing a severe differentiation disorder, 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, 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 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:

[0122] (a) administering to the individual an effective amount of a menin inhibitor, particularly 600 mg of zitomenib or a pharmaceutically acceptable form thereof per day;

[0123] (b) administering IV rehydration to the individual, and

[0124] (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.

[0125] 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.

[0126] Some embodiments comprise, prior to administering rasburicase, diagnosing the individual as having a high risk of having or developing a differentiation disorder by obtaining the following identification in the individual:

[0127] (i) having a white blood cell count level greater than or equal to about 100×10 9 / L, or

[0128] (ii) having a white blood cell count level (i) of about 25 to about 100×10 9 / L, or (ii) less than about 25×10 9 / L and a lactate dehydrogenase level greater than twice the upper limit of normal (e.g., where the normal level is about 280 units / L), and,

[0129] For each of (i) and (ii), wherein the individual has renal insufficiency, or uric acid, potassium, and / or phosphate levels above the applicable upper limit of normal.

[0130] 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, 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, 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 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:

[0131] (a) administering to the individual a prophylactic and / or effective amount of a corticosteroid, 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

[0132] (b) administering to the individual a therapeutically effective amount of a menin inhibitor.

[0133] 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.

[0134] In some embodiments, the corticosteroid and the menin inhibitor are administered daily, and are administered consecutively or simultaneously, optionally including administering the first dose of the corticosteroid and the menin inhibitor separately on or about the same day, or administering the first dose of the corticosteroid on a day before or after the first dose of the menin inhibitor.

[0135] In some embodiments, prior to administration of a corticosteroid or menin inhibitor, the individual has one or more of the following: a white blood cell count greater than 5×10 9 / L, increased serum creatinine level, severe extramedullary disease, and hyperplastic acute leukemia.

[0136] In some embodiments, the method comprises administering a corticosteroid daily starting on day one, administering a menin inhibitor daily starting on the same day or a subsequent day, and reducing the dose of the corticosteroid after about 28 days of administering the menin inhibitor if the individual has not been diagnosed with a differentiation disorder (in a risk reduction method) or if the individual has developed a differentiation disorder and the differentiation disorder improves and the level of bone marrow blasts is less than about 5% (in a risk reduction method or treatment method).

[0137] Some embodiments comprise administering dexamethasone (or an equivalent dose of an alternative oral or IV corticosteroid) to a subject intravenously at a dose of about 5, 10, or 15 mg, preferably 10 mg, or about 5 to 10 mg every 12 hours for one, two, or three days.

[0138] Some embodiments include if the individual's white blood cell count or leukocyte count increases to greater than about 10×10 9 / L or doubled, a therapeutically effective amount of hydroxyurea is administered to the individual, and optionally, a therapeutically effective amount of cytarabine, idarubicin, or gemtuzumab is administered to the individual.

[0139] Some embodiments comprise tapering the dose of and / or ceasing administration of the corticosteroid, hydroxyurea, cytarabine, idarubicin, or gemtuzumab following improvement of the differentiation disorder.

[0140] Some embodiments comprise interrupting administration of the menin inhibitor during all or part of the administration of one or more of IV rehydration, allopurinol, rasburicase, prednisone, dexamethasone, hydroxyurea, cytarabine, idarubicin, and gemtuzumab, and continuing after the differentiation disorder has improved (e.g., when the white blood cell count has dropped to less than about 20×10 9 / L) restart the menin inhibitor at a therapeutically effective dose or a reduced dose.

[0141] In some embodiments, the differentiation disorder is differentiation syndrome with or without leukocytosis. In some embodiments, the differentiation disorder is tumor lysis syndrome.

[0142] 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.

[0143] definition

[0144] The compounds of the present disclosure also include crystalline and amorphous forms of these 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, and mixtures thereof.

[0145] The compounds described herein may exhibit their natural isotopic abundance, or one or more atoms may be artificially enriched with a specific isotope having the same atomic number but an atomic mass or mass number different from the atomic mass or mass number primarily present in nature. All isotopic variants of the disclosed compounds, whether radioactive or not, are encompassed within the scope of this disclosure. For example, hydrogen has three naturally occurring isotopes, expressed as 1H (protium), 2H (deuterium), and 3H (tritium). Protium is the most abundant hydrogen isotope in nature. Enrichment with deuterium can provide certain therapeutic advantages, such as increasing half-life and / or exposure in vivo, or can provide compounds that can be used to study the in vivo pathways of drug elimination and metabolism. Isotopically enriched compounds can be prepared by conventional techniques well known to those skilled in the art.

[0146] The term "isotopologue" refers to an isotopically enriched compound. The term "isotopologue" refers to an isotopic composition of an atom in addition to its natural isotopic composition. An "isotopologue" may also refer to a compound containing at least one atom having an isotopic composition different from its natural isotopic composition. The term "isotopologue" refers to the amount of each isotope in a given atom. Radiolabeled and isotopically enriched compounds can be used as therapeutic agents (e.g., multiple myeloma therapeutics), research reagents (e.g., binding assay reagents), and diagnostic agents (e.g., in vivo imaging agents). All isotopic variants of the compounds described herein, whether or not radioactive, are intended to be encompassed within the scope of the embodiments provided herein.

[0147] "Isomers" refer to different compounds with the same molecular formula. "Stereoisomers" refer to isomers that differ only in the arrangement of their atoms in space. "Enantiomers" refer to a pair of stereoisomers that are mirror images of each other and are non-superimposable. A 1:1 mixture of a pair of enantiomers is a "racemic" mixture. The term "(±)" is used to indicate 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. Absolute stereochemistry is designated according to the Cahn-Ingold-Prelog RS system. When a compound is a pure enantiomer, the stereochemistry of each chiral carbon atom can be represented by R or S. For resolved compounds whose absolute configuration is unknown, it can be designated as (+) or (-) according to the direction of rotation (right-handed or left-handed) of plane polarized light at the wavelength of the sodium D line. Certain compounds described herein contain one or more asymmetric centers and can therefore give rise to enantiomers, diastereomers, and other stereoisomeric forms, whose asymmetric centers can be defined in terms of absolute stereochemistry as (R)- or (S)-. The chemical entities, pharmaceutical compositions, and methods of the present invention are intended to encompass all such possible stereoisomers, including racemic mixtures, optically pure forms, diastereomeric mixtures, 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 the compounds can be analyzed by any suitable method, including but not limited to chiral chromatography and optical rotation, and the degree of dominance of one stereoisomer over another can be determined.

[0148] Chemical entities with carbon-carbon double bonds or carbon-nitrogen double bonds can exist in Z or E forms (or cis or trans forms). In addition, some chemical entities can exist in various tautomeric forms. Unless otherwise indicated, chemical entities described herein also include all Z forms, E forms, and tautomeric forms.

[0149] The term "solvate" generally refers to a compound (eg, free base) or a salt thereof that further includes a stoichiometric or non-stoichiometric amount of a solvent bound by non-covalent intermolecular forces. When the solvent is water, the solvate is a hydrate.

[0150] The term "salt" or "pharmaceutically acceptable salt" refers to salts derived from various organic and inorganic counterions well known in the art. Pharmaceutically acceptable acid addition salts can be formed with inorganic 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 isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine and ethanolamine. In some embodiments, pharmaceutically acceptable base addition salts are selected from ammonium, potassium, sodium, calcium and magnesium salts.

[0151] The term "pharmaceutical composition" generally refers to a composition comprising a menin inhibitor (particularly zitomenib) in combination with at least one additional pharmaceutically acceptable carrier. A "pharmaceutically acceptable carrier" refers to a medium generally accepted in the art for delivering a biologically active agent to a subject, including, for example, adjuvants, excipients, or vehicles, such as diluents, preservatives, fillers, flow regulators, disintegrants, wetting agents, emulsifiers, suspending agents, sweeteners, flavorings, fragrances, antibacterial agents, antifungal agents, lubricants, and dispersants, depending on the mode of administration and the nature of the dosage form. Suitable carriers include, but are not limited to, any adjuvant, carrier, excipient, glidant, sweetener, diluent, preservative, dye, colorant, flavor enhancer, surfactant, wetting agent, dispersant, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier that has been approved by the United States Food and Drug Administration for use in humans or livestock.

[0152] Pharmaceutical compounds are formulated according to several factors within the skill of the art. These factors include, but are not limited to: the type and nature of the active agent being formulated; the subject to whom the pharmaceutical composition is to be administered; the intended route of administration of the composition; and the targeted therapeutic indication. Pharmaceutically acceptable carriers include aqueous and non-aqueous liquid media, as well as various solid and semi-solid dosage forms. In addition to the active agent, such carriers may contain a variety of different ingredients and additives, which are added to the formulation for a variety of reasons, for example, to stabilize the active agent, adhesives, etc., as is well known to those skilled in the art. Descriptions of suitable pharmaceutically acceptable carriers and the factors involved in their selection can be found in a variety of readily available sources, such as, for example, Allen, LV, Jr. et al., Remington: The Science and Practice of Pharmacy (Volume 2), 22nd edition, Pharmaceutical Press (2012).

[0153] As used herein, "treatment" or "treating" refers to an approach to obtaining a beneficial or desired result for a disease, disorder, or medical condition (e.g., AML), including but not limited to a therapeutic benefit and / or a prophylactic benefit in some cases. A therapeutic benefit refers to the eradication or amelioration of the underlying disorder being treated. A therapeutic benefit is also achieved by eradicating or ameliorating one or more physiological symptoms associated with the underlying disease, such that an improvement in the individual's condition is observed, even though the individual may still be suffering from the underlying disorder. In certain embodiments, to obtain a prophylactic benefit, a composition is administered to an individual at risk for a particular disease, or to an individual reporting one or more physiological symptoms of a disease, even though the disease may not have been diagnosed.

[0154] As used herein, the term "therapeutic effect" encompasses therapeutic benefits and / or prophylactic benefits 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, stopping or reversing the progression of a disease or condition, or any combination thereof.

[0155] As used herein, the term "effective amount," with respect to a compound, refers to an amount capable of treating, preventing, or managing a disorder, disease, or condition, or one or more symptoms thereof.

[0156] As used herein, the term "prophylactic amount" with respect to a compound refers to an amount capable of preventing a disorder, disease or condition, or one or more symptoms thereof, or lessening the ultimate severity of a disorder, disease or condition, or one or more symptoms thereof.

[0157] As used herein, the term "optimal biological dose" or "OBD" refers to the lowest dose of a drug, such as an investigational drug, that provides the highest rate of therapeutic efficacy while being safely administered.

[0158] As used herein, the term "recommended Phase 2 dose" refers to a dose of an investigational drug that has been accepted by a governmental agency (eg, the U.S. Food and Drug Administration (FDA) or similar agencies in other countries) for evaluation in a Phase 2 study.

[0159] As used herein, the term "safe and effective dose" refers to a dose of a drug (such as an investigational drug) that provides a clinical effect without unacceptable side effects.

[0160] As used herein, the term "maximum tolerated dose" refers to the highest dose of a drug (eg, investigational drug) that does not cause unacceptable side effects, eg, where the observed toxicity rate (eg, dose-limiting toxicity rate) is less than 0.33.

[0161] "Breakthrough therapy designation" refers to a designation granted by a government agency (e.g., the FDA or a similar agency in other countries) for an active pharmaceutical ingredient intended to treat a serious or life-threatening condition, and preliminary clinical evidence (e.g., Phase I clinical data) indicates that it may provide significant improvement over existing therapies on a clinically significant endpoint. In the United States, this status is known as Breakthrough Therapy Designation; in Europe, it is Priority Medicine or PRIME. As used herein, Breakthrough Therapy Designation may be for a specific indication and / or genetic subtype, such as NPM1-m AML.

[0162] An "investigational drug" is a substance that has been tested in laboratory experiments and has been approved for testing in humans by a government agency (such as the FDA or a similar agency in other countries).

[0163] "Chemotherapy" refers to the administration of one or more chemotherapeutic drugs and / or other agents to a subject by various methods, including intravenous, oral, intramuscular, intraperitoneal, intravesical, subcutaneous, transdermal, buccal, or inhaled, or in the form of a suppository. In the context of acute leukemia, chemotherapy is intensive chemotherapy, including a combination of anthracyclines (such as daunorubicin or idarubicin) and cytarabine, using a "7+3" regimen (cytarabine for 7 consecutive days and a short-term infusion of anthracyclines daily for the first 3 days).

[0164] "Subject" refers to an animal, such as a mammal, for example, a human. The methods described herein can be used for therapeutic and veterinary applications in humans. In some embodiments, the subject is a mammal, and in some embodiments, the subject is a human. "Mammal" includes humans and domestic animals, such as laboratory animals and household pets (e.g., cats, dogs, pigs, cattle, sheep, goats, horses, rabbits), and non-domestic animals, such as wild animals, etc. In some embodiments, the age of the human is ≥18 years old. In some embodiments, the age of the human is less than 18 years old, less than 12 years old, less than 6 years old, 5 years old, 4 years old, 3 years old, 2 years old or 1 year old.

[0165] Clinical terms used in this article include the following: "CR" refers to complete remission, with no visible evidence of leukemia cells in the blood or bone marrow, normal bone marrow function, and normal numbers of healthy blood cells returning to the blood circulation as confirmed by bone marrow biopsy and blood tests; the CR rate is defined as the group of patients who achieve the best overall response of CR; "CRh" refers to a complete response with hematologic recovery; the CR / CRh response rate is defined as the proportion of patients who achieve a best overall response of CR (with or without MRD) or CRh; "CRi" refers to a complete response with incomplete hematologic recovery; "CRp" refers to a complete remission with incomplete platelet recovery; CRc refers to a composite complete remission, and the response rate is defined as the proportion of patients who achieve a best overall response of CRi (including CRp), CRh, or CR (including MRD-); "MRD" refers to measurable residual disease and refers to the level of leukemia that is not easily visible under a microscope but can be detected by laboratory methods. CR can be with or without measurable disease (CR MRD+ / MRD-); "MLFS" refers to morphologically leukemia-free status; "PR" refers to partial response; "SD" refers to stable disease without progression; "ORR" refers to overall response rate and is determined by the following formula: ORR=CR (including CR MRD-)+CRh+MLFS (including CRp).

[0166] "BC" stands for 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 contains no blasts. A blast level of at least 20% in the bone marrow or blood usually suggests a diagnosis of AML.

[0167] Hydroxyurea, or hydrea, is an antimetabolite that prevents the overproduction of blood cells in proliferative diseases and is useful in reducing elevated levels of leukemic white blood cells in AML.

[0168] "DS" refers to differentiation syndrome, a potentially serious side effect that can occur in people with acute leukemias (such as AML) who are treated with certain types of anticancer drugs. Differentiation syndrome usually develops within 1-2 weeks of starting treatment. It is caused by the large, rapid release of cytokines by leukemia cells affected by the anticancer drugs. Signs and symptoms of differentiation syndrome include fever, cough, difficulty breathing, weight gain, swelling of the arms, legs, and neck, excess fluid buildup around the heart and lungs, low blood pressure, and kidney failure.

[0169] "SCT" or "HSCT" refers to hematopoietic stem cell transplantation. In some embodiments of the methods provided herein, the subject receives SCT after receiving treatment or administration of zitomenib or a pharmaceutically acceptable form thereof. In some embodiments of the methods provided herein, the subject has received SCT before receiving treatment or administration of zitomenib or a pharmaceutically acceptable form thereof. In some embodiments, zitomenib or a pharmaceutically acceptable form thereof is administered to the subject before and after SCT (e.g., as maintenance therapy).

[0170] Extramedullary hematopoiesis refers to the formation and activation of blood cells outside the bone marrow and is a response to hematopoietic stress caused by leukemia.

[0171] As used herein, the terms "co-administration," "combination administration," and their grammatical equivalents encompass the administration of two or more pharmaceutical agents to an animal (including a human) such that both agents and / or their metabolites are present in the subject's body at the same time. Co-administration includes simultaneous administration in different compositions, administration at different times in different compositions, or administration in a composition in which both agents are present.

[0172] The terms "antagonist" and "inhibitor" are used interchangeably and refer to compounds that are capable of inhibiting a biological function (e.g., activity, expression, binding, protein-protein interaction) of a target protein (e.g., menin, MLL1, MLL2 and / or MLL fusion protein). Thus, the terms "antagonist" and "inhibitor" are defined in the context of the biological effects of the target protein. Although preferred antagonists herein interact specifically with (e.g., bind to) the target, compounds that inhibit the biological activity of the target protein by interacting with other members of the signal transduction pathway to which the target protein belongs are also expressly included in this definition. Preferred biological activities inhibited by the antagonist are related to the development, growth, or spread of a tumor.

[0173] As used herein, the term "agonist" refers to a compound that is capable of activating or enhancing the biological function of a target protein, whether by inhibiting the activity or expression of the target protein. Thus, the term "agonist" is defined in the context of the biological action of a target polypeptide. Although preferred agonists herein interact specifically with (e.g., bind to) a target, compounds that activate or enhance the biological activity of a target polypeptide by interacting with other members of the signal transduction pathway to which the target polypeptide belongs are also explicitly included in this definition.

[0174] "Signal transduction" refers to the process by which stimulatory or inhibitory signals are transmitted into and within cells to elicit an intracellular response. Signal transduction pathway modulators are compounds that modulate the activity of one or more cellular proteins that are located in the same specific signal transduction pathway. Modulators can enhance (agonists) or inhibit (antagonists) the activity of signaling molecules.

[0175] As used herein, "sample" includes and / or refers to any fluid or liquid sample used for analysis to detect and / or quantify an analyte. In some embodiments, the sample is a biological sample. Examples of samples include, but are not limited to, body fluids, extracts, solutions containing protein and / or DNA, cell extracts, cell lysates, or tissue lysates. Non-limiting examples of body fluids include urine, saliva, blood, serum, plasma, cerebrospinal fluid, tears, semen, sweat, pleural effusions, liquefied feces, and lacrimal secretions.

[0176] The term "in vivo" refers to events that occur within the body of an individual.

[0177] The term "in vitro" refers to an event that occurs outside the body of a subject. For example, an in vitro assay encompasses any assay performed outside the body of a subject. In vitro assays encompass cell-based assays, in which live or dead cells are used. In vitro assays also encompass cell-free assays, in which intact cells are not used.

[0178] 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. Also as used herein, "comprising" may be replaced with "consisting essentially of" and / or "consisting of" in any case or embodiment described herein.

[0179] As used herein, the term "and / or" should be understood as specific disclosure of each of the two specified features or components (regardless of whether the other is present). For example, "A and / or B" should be understood as specific disclosure of each of (i) A, (ii) B, and (iii) A and B, just as if each were individually listed herein.

[0180] As used herein, the term "about" when used in connection with a dose, amount or weight percentage means that the dose, amount or weight percentage is within 10%, or within 5%, or within 2%, or within 1% of the stated amount.

[0181] When numerical values are used herein, such values may encompass a range of ±5% of the stated numerical value.

[0182] Example

[0183] The following examples are included for illustrative purposes only and are not intended to limit the scope of the present disclosure.

[0184] Example 1 - Analysis of Zitomenid Concentrations in Mouse Tissues and Plasma

[0185] Following 8 days of oral gavage administration of zitomenib to female C57BL / 6 mice, zitomenib concentrations were measured in plasma, bone marrow, heart, and spleen. A group of five animals was treated with 100 mg / kg of zitomenib orally daily for 8 days. Bone marrow, spleen, plasma, and heart samples were collected 24 hours after dosing on day 8. Each sample was processed as follows:

[0186] Blood collection and processing: Blood samples (approximately 0.03 mL) were collected from the great saphenous vein or other appropriate site of each animal and placed in pre-cooled commercial EDTA-K2 tubes or pre-cooled plastic microcentrifuge tubes containing 2 μL of 0.05 M EDTA-K2 as an anticoagulant and placed on wet ice until centrifugation. Blood samples were processed by centrifugation at approximately 4°C and 3,200 × g for 10 minutes to extract plasma. Plasma was collected and transferred to pre-labeled 96-well plates or polypropylene tubes, flash-frozen on dry ice, and stored at -60°C or lower until analysis. LC-MS / MS was used for analysis.

[0187] Tissue processing Tissue samples for drug level analysis were homogenized on wet ice with homogenization buffer (MeOH / 15 mM PBS, 1:2) at a 1:9 ratio (1 g tissue to 9 mL buffer). Homogenates were stored at -60°C or lower until analysis. LC-MS / MS analysis was performed.

[0188] like Figure 1 As shown, the analysis revealed that zitomenib accumulated to higher levels in tissues compared to plasma.

[0189] Example 2 - Plasma protein binding of Zitomenid

[0190] Zitomenid or the positive control warfarin was spiked into CD-1 mouse and human plasma. Zitomenid was tested at concentrations of 0.2, 2, and 10 μM, and warfarin was tested at 2 μM. Spiked plasma samples were preincubated at 37 ± 1°C and then centrifuged to precipitate plasma proteins and separate them from free compounds in the supernatant. LC-MS / MS was used to determine the concentrations of zitomenid and warfarin in spiked plasma and supernatant samples. % unbound, % bound, and % residual were calculated according to the following formulas:

[0191]

[0192] Where [F] is the free compound concentration or the analyte / internal standard peak area ratio in the protein-free sample after ultracentrifugation; [T0] is the compound concentration or the analyte / internal standard peak area ratio in plasma at time zero; and [T4.5] is the compound concentration or the analyte / internal standard peak area ratio in plasma after 4.5 hours of incubation.

[0193] Zitomenid plasma protein binding was determined to be greater than 99%.

[0194] Example 3 - Phase 1 / 2 First-in-Human Study of the Menin-MLL (KMT2A) Inhibitor KO-539 (Zitomenib) in Patients with Relapsed or Refractory (R / R) Acute Myeloid Leukemia (AML) (NCT 04067336)

[0195] A. Background

[0196] KO-MEN-001 is a first-in-human, open-label, multi-cohort study of zitomenib in adult patients with R / R AML, consisting of an initial dose-escalation portion (Phase 1a) and a dose-confirmation / cohort expansion portion (Phase 1b).

[0197] The Phase 1a dose-escalation trial enrolled 30 adult patients with R / R AML, regardless of genotype (all cohort). Patients received 50 mg (1 patient), 100 mg (1 patient), 200 mg (6 patients), 400 mg (5 patients), 600 mg (5 patients), 800 mg (11 patients), or 1000 mg (1 patient) of zitomenib once daily to evaluate safety, tolerability, and anti-leukemic activity (CR / CRh, CR with or without measurable residual disease (MRD), duration of response (DOR), event-free survival, and overall survival (OS)) across a range of zitomenib dose levels and to determine the maximum tolerated dose (MTD) and / or recommended phase 2 dose (RP2D) (optimal biologically effective dose) of zitomenib in patients with R / R AML, regardless of genotype. The median age of the subjects was 65.5 years (range, 22-85), 33% (10 patients) had KMT2A-r AML, and 13% (4 patients) had NPM1-m AML (non-KMT2A-r / NPM1-m, 16 (53%)). Patients were heavily pretreated and had received a median of 3.5 prior lines of therapy (range, 1-9). Most patients had previously received venetoclax, and 23% had received ≥1 prior stem cell transplant (SCT).

[0198] The Phase 1b dose-confirmation portion of the study explored the two lowest doses that had demonstrated meaningful activity in the Phase 1a study, 200 mg and 600 mg of zitomenib once daily, in KMT2A-r or NPM1-m AML to explore the potential for optimal biologically active doses in these patient populations. The median age of the first 36 subjects enrolled (NPM1-m, 17; KMT2A-r, 19; and co-mutations including IDH and FLT3, primarily in NPM1-m patients) was 52 years (range, 28-84), and approximately one-third of the subjects had at least one prior SCT. Patients received a median of three prior therapies (range, e.g., 1 to 12 for KMTA2-r and 2 to 8 for NPM1-m for the first 24 patients), with 66.7% of patients receiving venetoclax prior to enrollment and 30.6% receiving a prior SCT.

[0199] The demographic data of the first 53 patients accrued in Phase 1b are shown in Table 1 .

[0200] Table 1.

[0201]

[0202]

[0203] *Patients can have both FLT3 and IDH1 / 2 and be counted in both co-mutation categories.

[0204] For the 53 patients in phase 1b, the patients either withdrew from the study during the first cycle or had already received at least one cycle of treatment; the patient disposition is shown in Table 2.

[0205] Table 2.

[0206]

[0207] **None of the adverse events were considered to be treatment-related.

[0208] Approximately 30% of patients remain on treatment, and nearly 50% remain in follow-up. The most common reason for patient discontinuation was underlying disease progression. Although six patients discontinued due to adverse events, none of these events were considered treatment-related.

[0209] In both parts, zitomenib was administered orally once daily for 28 days.

[0210] Study Participants—Analysis Group

[0211] In this Phase 1 study, the population for clinical safety and efficacy analysis was the modified intention-to-treat (mITT) population: all patients who received at least one dose of study drug. Patients were grouped into the mITT population based on dosing cohort and tumor genetics. The following subgroups were used in the analysis:

[0212] The KMT2A-r subgroup in the 200 mg and 600 mg dose cohorts in the mITT Phase 1a and Phase 1b combination trials; and

[0213] • NPM1-m subgroups of the 200 mg and 600 mg dose cohorts in the mITT Phase 1a and Phase 1b combination trials.

[0214] Where appropriate, data from the following patient subgroups of the analysis population are presented in this example:

[0215] Group 1: Phase 1a (all patients in the mITT set at the time of data cutoff);

[0216] Group 2: Phase 1b (all patients in the mITT cohort at the time of data cutoff);

[0217] Cohort 3: patients with on-target mutations in Phase 1a (e.g., patients with KMT2A-r or NPM1-m AML) plus all patients in the Phase 1b mITT set at the time of data cutoff (all on-target cohort); and

[0218] • Group 4: Phase 1a patients with on-target mutations plus the first 24 patients (or up to 53 total, if specified) who were enrolled in Phase 1b (on-target maturation cohort) and who have received at least 2 months of follow-up.

[0219] These patient groups allow for the assessment of safety in patients regardless of mutation status (Group 1), safety and efficacy in the target patient population (Groups 2-4), and efficacy signals in patients to support the determination of an RP2D and who have been on treatment for an adequate time to achieve a potential clinical benefit / response (Group 4).

[0220] B. Antileukemic activity

[0221] In the Phase 1a portion of this study, clinical benefit was demonstrated across all genotypes evaluated, with 30% of R / R A M L patients continuing to receive at least four cycles of treatment with disease control (e.g., reduction in blast counts [BC] or reduced requirement for hydroxyurea), and overall improvement in patient performance status was observed across all dose levels. At 100 mg, a complete response (CR) was observed in one patient with both SETD2 and RUNX1 mutations, suggesting that other AML genotypes may be dependent on the menin pathway. At 200 mg, two NPM1-m patients responded positively: one patient experienced a CR (no measurable residual disease [MRD-]) of at least 100 weeks duration, and one patient with both NPM1-m and FLT3-ITD mutations achieved morphologic leukemia-free status [MLFS]. At the 600 mg and 800 mg doses, KMT2A-r patients achieved stable disease with significant reductions in BC and prolonged duration of improved performance status (e.g., one patient's response lasted for more than four months). Clinical benefits observed in the Phase 1a portion included 29% continuing to receive at least four cycles of treatment, reductions in blast counts (RUNX1 mutation), reduced need for hydroxyurea (one KMT2A-r subject), and overall improvement in patient performance status across dose levels.

[0222] Clinical efficacy in the Phase 1b portion of this trial was dose-dependent. Response rates with the 600 mg dose once daily (QD) consistently demonstrated increased antileukemic activity compared to the 200 mg dose QD. In target patients in Phase 1a and the first 24 patients enrolled in Phase 1b, complete remission (CR) / with partial hematologic recovery (CRh) and composite CR rates were 21.4% and 6.7% at 600 mg and 28.6% and 6.7% at 200 mg, respectively (1a) and 24 at 1b. At 200 mg, changes in bone marrow morphology and stabilization / reduction in blast counts were observed. Three patients had improvements with a dose increase to 600 mg: one achieved a bone marrow blast count <5% and a significant reduction in the high burden of extramedullary disease despite the persistence of small lesions; one had a significant reduction in BC and disease control; and one achieved MLFS and continues treatment. At 600 mg, 25% of the first 24 Phase 1b patients had a best response of CR or CR with partial hematologic recovery (CRh), including 33.3% of NPM1-m patients who achieved CR or CRh. For the first 24 Phase 1b patients, the composite CR was 33%, with 75% measurable residual disease (MRD), and the overall response rate (ORR) was 42%.

[0223] As of October 2022, Phase 1b recruitment has been completed (N=53), and 30% (including 21% at the 600 mg dose) are still undergoing treatment and gradually gaining clinical benefit. Although the 200 mg dose showed some efficacy in the NPM1-m patient population, KMT2A-r patients did not show any formal response. The overall efficacy signal is shown in Table 3, with an overall CR / CRh of 21.2%, CRc of 26.3%, and ORR of 28.9% in the pooled group. In this expanded group of patients, a total of 20 NPM1-m patients were recruited and treated with 600 mg of zolpidem. This subgroup continued to show strong evidence of anti-leukemia activity, with a CR / CRh of 30.0%, a CRc of 35.0%, and an ORR of 40.0%. Although 43% of patients who achieved CRc also achieved MRD negativity, only 5 of them underwent MRD testing. Of these tested patients, 60% were MRD negative. Among patients with a CR / CRh, two-thirds had IDH and / or FTL3 co-mutations. Overall, 57% of the seven patients with IDH co-mutations achieved a CR with zitomenib. Furthermore, the ORR for patients who developed differentiation syndrome was 75% across all arms. Although significant activity was observed in patients with KMT2A-r, only one patient achieved a formal CR / CRh response, resulting in an ORR of 16.7%.

[0224] Table 3. Summary of responses in all patients treated with 200 mg and 600 mg of 58 patients from Phase 1a / 1b with target mutations.

[0225]

[0226] n / N = number of patients; 5 / 7 CRc patients underwent MRD assessment; 3 (60%) of those tested were MRD negative; CRc includes CR, CRh, CRi, CRp; ORR includes CR, CRh, CRi, CRp, MLFS.

[0227] C. Safety and Tolerability

[0228] Dosage safety and tolerability

[0229] There was no clear association between zitomenib dose and the rate of treatment-emergent adverse events (TEAEs), regardless of severity, severity, or relevance. Overall, events were consistent with the role of the underlying disease. The rates of TEAEs and serious adverse events (SAEs) are shown in Table 4. Although there were numerical differences between the dosing groups, there was no significant increase in the rate or severity of AEs with increasing dose.

[0230]

[0231] The most common TEAEs reported in ≥15% of patients were similar in Phase 1a and Phase 1b 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.

[0232] TEAEs by severity (≥Grade 3)

[0233] In Phase 1a, 11 of 11 patients (100%) reported at least one TEAE, and 26 of 30 patients (86.7%) reported TEAEs of Grade ≥3, regardless of causality. The most common TEAEs of Grade ≥3 were anemia (8 patients [26.7%]) and pneumonia (7 patients [23.3%]), followed by febrile neutropenia, neutropenia, thrombocytopenia, and decreased appetite (3 patients [10.0%] each). 8 patients (26.7%) reported a Grade ≥3 TEAE considered by the investigator to be related to zitomenib (1 patient each at 50 mg, 100 mg, 200 mg, 400 mg, 600 mg, and 1000 mg, and 2 patients at 800 mg). The most common Grade ≥3 zitomenib-related TEAE reported in Phase 1a patients was pulmonary embolism (2 patients [6.7%]). The TEAEs ≥ Grade 3 by dose for Phase 1a are shown in Table 5.

[0234] Table 5. Grade ≥3 TEAEs (all causal relationships)

[0235]

[0236] 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 1a. Two DLTs were reported: (1) in the 400 mg group (pneumonitis, post-aspiration pneumonia); and (2) in the 1000 mg group (differentiation syndrome).

[0237] For the first 24 patients in the Phase 1b portion of this study, TEAEs of grade 3 or higher occurring 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 leukocytosis (13% each). At 200 mg (N=12), TEAEs of grade 3 or higher occurring 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), Grade ≥3 TEAEs occurring in ≥10% of patients included febrile neutropenia and anemia (25% each); and DS, leukocytosis, neutropenia, thrombocytopenia, leukopenia, and diarrhea (17% each).

[0238] For the first 36 patients in Phase 1b, 34 of 36 patients (94.4%) reported at least one TEAE, of which 28 patients (77.8%) reported a grade ≥3 TEAE, regardless of causality. The most common TEAEs ≥ grade 3 were febrile neutropenia (7 patients [19.4%]), DS and anemia (6 patients [16.7%] each), as well as pneumonia, sepsis, and decreased platelet count (4 patients [11.1%] each). Fifteen patients (41.7%) reported a grade ≥3 TEAE that the investigator considered to be related to zitomenib, including 7 patients (41.2%) in the 200 mg group and 8 patients (42.1%) in the 600 mg group. The most common grade ≥3 zitomenib-related TEAE reported in Phase 1b patients was DS (6 patients [16.7%]). Twenty-three patients (63.9%) reported SAEs (regardless of causality), and 11 patients (30.6%) reported SAEs that the investigator considered to be related to zitomenib (five patients [29.4%] in the 200 mg cohort and six patients [31.6%] in the 600 mg cohort). No patients reported TEAEs requiring dose reduction, and the rates of patients requiring dose interruption or discontinuation were similar between the 200 mg and 600 mg zitomenib dose levels (41.2% vs. 31.6% and 11.8% vs. 10.5%, respectively). Serious adverse events identified as related to zitomenib 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.

[0239] In the 53 subjects in the Phase 1b portion, grade 3 or higher adverse events, regardless of causality, occurring in greater than 10% of patients were rare. TEAEs of grade 3 or higher occurring 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 leukocytosis (13% each). At 200 mg (N=12), TEAEs of grade 3 or higher occurring 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 occurring in ≥10% of patients were febrile neutropenia and anemia (25% each); and differentiation syndrome, leukocytosis, neutropenia, thrombocytopenia, leukopenia, and diarrhea (17% each).

[0240] No reports of QTc prolongation were observed in Phase 1b, and overall, no clinically meaningful trends were observed in clinical laboratory assessments, vital signs, or ECGs.

[0241] In summary, the pooled safety data from 36 patients collected during Phase 1b at the time of data cutoff were consistent with the Phase 1a data, demonstrating comparable safety and tolerability between the 200 mg and 600 mg zitomenib monotherapy doses.

[0242] Safety and tolerability according to genotype

[0243] When assessed by genetic subtype, safety results for KMT2A-r and NPM1-m AML patients who received 200 mg or 600 mg of zitomenib in Phase 1a and Phase 1b were generally consistent with the overall study population (Table 6), indicating no significant relationship between zitomenib dose and the overall frequency of TEAEs. The most common TEAEs of grade ≥ 3 were anemia, febrile neutropenia, pneumonia, sepsis, increased alanine aminotransferase, decreased platelet count, and differentiation syndrome for KMT2A-r patients, and anemia, neutropenia, thrombocytopenia, diarrhea, pneumonia, sepsis, decreased neutrophil count, decreased white blood cell count, and hyperglycemia for NPM1-m patients. However, the risk of serious adverse events increased to 70.8% for the KMT2A-r cohort, compared to 52.9% for the NPM1-r cohort. Serious adverse events occurring 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 incidence was not dose-related. The incidence of dose-limiting toxicity was 30.0% for KMT2A-r and 14.3% for NPM1-m.

[0244] Table 6. Summary of Patient-Emerging Adverse Events by Genotype - Phase 1a and 1b Combined - mITT Pool

[0245]

[0246] Abbreviations: See Table 4.

[0247] For each AE category (TEAEs, Grade 3+ TEAEs, and SAEs), the reported event rates and severity were consistent across dose groups. Combined with the limited number of TEAE-related dose interruptions and / or discontinuations, the data suggest that the tolerability of zitomenib does not decrease with increasing dose, and the safety and tolerability profile is comparable between the 200 mg and 600 mg zitomenib doses. When assessed by genetic subtype, safety results in patients with KMT2A-r and NPM1-m AML who received 200 mg or 600 mg were generally consistent with the overall study population, and there was no apparent relationship between zitomenib dose and the overall frequency of TEAEs. With the exception of the DS discussed further below, the reported events appeared to be common or related to the underlying disease.

[0248] Differentiation syndrome

[0249] Given that inhibition of menin activity disrupts gene expression pathways that maintain the pathological dedifferentiated stem-like phenotype of KMT2A-r and NPM1-m AML, TEAEs of DS are considered treatment-related and attributable to the effects of zitomenib on cancer cells. DS responses must be carefully managed to ensure patient safety and continued access to therapy.

[0250] In Phase 1a, an event of on-target effect (grade 4) of DS was reported in a KMT2A-r patient at the 1000 mg dose level, leading to a reduction in the 1000 mg dose group and completion of Phase 1a enrollment at the 800 mg dose. Of the first 24 patients in Phase 1b, seven patients experienced DS, including three patients at 200 mg of KMT2A-r, two of whom experienced grade 3 events, including one death; and four patients at 600 mg, two of whom experienced grade 3 DS (one KMT2A-r and one NPM1-m), and two of whom were grade 2 (one KMT2A-r and one NPM1-m). DS guidelines were developed, and implementation resulted in a reduction in the severity of reported DS events.

[0251] The Norsworthy algorithm (Norsworthy, 2020) was applied to review data for potential events of DS that were not identified by all investigators and are listed in Table 7 along with cases identified by the investigators. As shown in Table 7, among the first 36 patients in Phase 1b, the investigator-reported DS rate remained consistent between the 200 mg and 600 mg dose levels (29.4% vs. 26.3%, respectively). In Phase 1b, the rate of severe DS 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 that the severity of DS did not increase with increasing dose.

[0252] Table 7. Differentiation syndrome in stage 1b - mITT panel

[0253]

[0254] Abbreviations: DS = differentiation syndrome; n / N = number of patients; Pts = patients.

[0255] While the overall safety profile across genetic cohorts was consistent across the study population and independent of dose, a genetic subtype-dependency in DS was observed, as shown in Table 8, with KMT2A-r patients more likely to experience this event. Of the 10 total cases of DS reported through the Phase 1b time point of 36 patients, 7 (70.0%) occurred in KMT2A-r patients, suggesting that KMT2A-r patients are potentially more susceptible to DS-type events. Furthermore, the rate of severe DS reported in KMT2A-r patients was increased compared to the NPM1-m subgroup overall (20.8% for KMT2A-r and 5.9% for NPM1-m), and this was true at both the 200 mg and 600 mg zitomenib dose levels. When DS occurred in NPM1-m subjects, it was generally moderate in severity and resolved with appropriate intervention.

[0256] Table 8. Differentiation Syndrome by Genotype at 200 mg and 600 mg Zitomenib Dose Levels Phase 1a and Phase 1b - mITT Pool

[0257]

[0258] Abbreviations: See table above.

[0259] For the 53-subject cohort, Grade 3+ TEAEs occurring in >10% of participants by genetic subtype and dose in Phase 1b (regardless of causality assessment) are shown in Table 9. Grade 3 or higher adverse events occurring in >10% of patients, regardless of causality, were rare. No such events were reported in the NPM1-m population. For KMT2A-r patients, differentiation syndrome was reported in 25% at the 600 mg dose, and febrile neutropenia was reported in 13%.

[0260] Table 9.

[0261]

[0262] The incidence and severity of differentiation syndrome by genotype in 53 subjects in Phase 1a / 1b at the 200 mg and 600 mg doses are shown in Table 10.

[0263] Table 10.

[0264]

[0265] As shown above, 20% of patients receiving NPM1-m at 600 mg experienced differentiation syndrome, a quarter of which were at least grade 3. For KMT2A-r patients, the incidence was similar across doses, with approximately 38% experiencing differentiation syndrome and 25-30% experiencing grade 3 or higher events. Among patients experiencing differentiation syndrome at the 600 mg dose, the ORR rate was 75% for NPM1-m and 16.7% for KMT2A-r.

[0266] There are other less reported adverse events (increased alanine aminotransferase, pleuritic chest pain, myocarditis) that may be associated with DS events. These adverse events occurred almost entirely in KMT2A-r patients. Since KMT2A-r disease is usually a monocytic disease and is therefore aggressive, it may be associated with extramedullary disease that is not always identified at baseline. (Fianchi et al., Mediterrr. J. Hematol Infect Dis. 2021, 13 (1), e2021030.) Since zitomenib is concentrated in tissues, these events may and are suspected to be related to the differentiation of zitomenib-induced leukemia cells in disease-related extramedullary sites, rather than an indication of disease progression.

[0267] These data suggest that differentiation syndrome represents the most significant adverse effect associated with zitomenib therapy. It showed no evidence of dose-dependency, however, there was a clear association between KMT2A-r disease and NPM1-m AML. In the genetically enriched Phase 1b cohort, the occurrence of DS was not dose-dependent, but rather genetic subtype-dependent, and KMT2A-r patients were more likely to experience this event. It is suspected that due to the monocytic nature and therefore aggressive nature of KMT2A-r leukemia, these patients have a higher degree of undiagnosed extramedullary disease and are accompanied by higher levels of organ involvement (including heart, liver, and other organs). Menin inhibitor-associated DS (such as those induced by zitomenib) has not been previously reported and can manifest as bone pain, transient pain in the extremities, initial elevations in liver function tests, cardiac inflammatory events, and transient changes in other organ function, all of which are potentially related to differentiation of previously unrecognized extramedullary disease. The aggressiveness of monocytic disease is well known, and KMT2A-r patients have higher levels of extramedullary involvement compared to patients with AML of other genotypes, which supports this view. (Kapur et al., Leuk. Res. Rep. 2022, 18, 100349.)

[0268] At the time of submission, Phase 1b enrollment was complete (N=53) and 21% (all at the 600 mg dose) remained on treatment and continued to experience clinical benefit. The overall safety profile of the expansion cohort was consistent with that described above. No new cases of DS were reported or detected by the DS algorithm in NPM1-m subjects since the last data cutoff (N=3 datasets / 4 safety databases).

[0269] Findings made during the study provide insights into developing treatment strategies to maximize the duration of treatment for patients. Notably, leukocytosis has been shown to be frequently misdiagnosed as disease progression or DS, and changes in peripheral blasts are similarly unpredictable. Controlling DS episodes is associated with a higher likelihood of clinical benefit. Although uncommon, when these events occur in NPM1-m patients, they can be managed with improved DS monitoring and treatment approaches, resulting in rapid remissions and often predicting leukemia clearance (~75% of NPM1-m patients who experience DS events achieve CR / CRh / CRi (ORR), in part by allowing patients to continue treatment for at least two cycles). The emergence of specific DS monitoring and treatment strategies has helped identify unique manifestations of DS associated with menin inhibitors and manage them in a way that enables patients to continue treatment.

[0270] D. Blood chemistry

[0271] The mean changes from baseline in peripheral blasts and leukocytes in the target population for the 600 mg dose (Phase 1a and Phase 1b) during Cycle 1 (28 days) showed a transient increase in these blood chemistry markers during the first one to two weeks, followed by a decrease over the remainder of the first cycle, as shown in Table 1. Figure 2 As shown. Although not always associated with DS events or predicting progression, early increases in white blood cell (WBC) counts and peripheral blasts appear to be associated with drug activity, providing a context for the rapid onset of DS-type symptoms after treatment initiation. Recognizing that DS symptoms are indicators of drug action, mitigation measures are implemented to enable patients to continue treatment. Although managed DS can predict patient response, with 75% and 17% of NPM1-m and KMT2A-r patients, respectively, ultimately achieving ORR events, differences in the severity of DS are observed between different genetic subtypes. The different responses may be due to the disseminated nature of KMT2A-r disease, which extensively infiltrates the extramedullary space. As shown in Example 1, zitomenib accumulates at higher levels in tissues. This high tissue permeability can lead to diffuse and unpredictable DS symptoms (e.g., diffuse pain) in KMT2A-r patients. Implementation of DS guidance results in better identification of DS events and earlier intervention.

[0272] E. Exposure and Biomarkers

[0273] Intensive or sparse pharmacokinetic sampling was performed after the first dose (Cycle 1, Day 1) and at steady state (Cycle 2, Day 1). Steady-state trough samples (predose) were collected on Days 8 and 15 of Cycle 1 and, when possible, in subsequent cycles. Concentrations of zitomenib and certain active metabolites were determined by validated liquid chromatography / mass spectrometry assays. The following parameters were determined: AUC 0-24-ss (area under the plasma concentration-time curve during the dosing interval at steady state), C 谷值-ss (trough plasma concentration measured at the end of the dosing interval at steady state) and C 最大值-ss (maximum concentration at steady state). An exposure-response analysis was performed on 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 panels AC of Figure 3, a dose-dependent increase in exposure was observed with the 600 mg dose compared to the 200 mg dose. However, the exposure of zitomenib was comparable at the 600 mg and 800 mg doses. Based on these studies, any further increase in dose above 600 mg QD is not expected to increase the likelihood or magnitude of response.

[0274] Changes in MEIS1 expression on day 28 of cycle 1 were measured as a pharmacodynamic biomarker of zitomenib inhibition of menin transcriptional signaling. Bone marrow aspirates collected during screening and at the end of zitomenib dosing in cycle 1 were evaluated for MEIS1 expression levels. Changes in MEIS1 expression were determined using quantitative RNA sequencing. Because patients who achieved a CR at the time of bone marrow biopsy had no leukemic cells and were expected to have low MEIS1 expression, this was not evaluated. Figure 4A As shown, at the end of cycle 1, the four patients who received the 600 mg dose had a reduction of more than 85% in MEIS1 expression, while the two patients who received the 200 mg dose had no detectable reduction in MEIS1 expression. Figure 4B As shown, on cycle 1, day 28, MEIS1 expression in KMT2A-r and NPM1-m patients was reduced to 1 / 6 and 1 / 8, respectively, with 600 mg administration compared to 200 mg. Target gene expression at the 800 mg dose did not provide evidence of further knockdown.

[0275] In addition, the expression of other menin target genes, such as HOXA9, HOXA10, and MEF2C, was reduced by 1 / 2 to 1 / 6 at 600 mg compared to 200 mg. RNAseq data showed that the 600 mg dose had a stronger inhibitory effect on the menin pathway, providing supportive evidence that 600 mg administration is superior to 200 mg.

[0276] Population pharmacokinetic analysis determined that coadministration of CYP3A4 inhibitors, renal or hepatic status, patient mutations, and ECOG status were not significant covariates affecting pharmacokinetics.

[0277] F. Supplementary clinical research data

[0278] Supplement 1.

[0279] This report provides an update on the duration of response (DoR) for patients with Ph 1NPM1-m who received the 600 mg RP2D dose (n=20) as of January 31, 2023, and for those who received the 200 mg RP2D dose. The median age of patients receiving the 600 mg RP2D was 70.5 years (range, 22 to 86 years). FLT3 and IDH1 / 2 mutations were common (35% for FLT3 and 30% for IDH1 / 2, respectively); 20% had co-mutations of FLT3 and IDH1 / 2. The median number of prior therapies was 2.5 (r: 1 to 8), including 15% who had received ≥1 prior stem cell transplant (SCT) and 60% who had received venetoclax.

[0280] The cumulative safety profile of zitomenib 600 mg RP2D was consistent with previous reports, with no new signals observed. The majority of subjects (85%) experienced at least one grade ≥3 treatment-emergent adverse event (TEAE), of which 30% were considered potentially treatment-related. The most common (>10%) TEAEs grade ≥3 were anemia (25%), pneumonia (20%), thrombocytopenia, neutropenia, and hyperglycemia (15% each). In NPM1-m patients, 20% reported differentiation syndrome (DS) events of any grade, and 5% (n=1) experienced grade 3 DS.

[0281] As of January 31, 2023, the complete remission (CR) rate for patients receiving 600 mg of NPM1-m was 30% (6 patients; 95% CI 12-54%), the CR rate and CR / CRh rate 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 who achieved CRc underwent MRD assessment; of the 7 patients who underwent MRD assessment, 60% were MRD-negative), and the ORR rate was 40% (8 patients; 95% CI 19-64%). According to Kaplan-Meier (KM) estimates, the median duration of response for patients who achieved CRc (continued to mature) was 8.2 months (95% CI: 1.5 to NE). One CR was observed at the 200 mg dose, with a DoR lasting 32 cycles. The median time to CR for NPM1-m patients at the RP2D was 70 days (r: 26 to 89). Two patients (1 CR and 1 CR with incomplete hematologic recovery [CRi]) went on to receive SCT and were both in remission at cutoff. The median overall survival for NPM1-m patients treated with 600 mg was 5.1 months (95% CI: 2.1 to NE), with a median follow-up duration of 8.0 months. As of cutoff, 57.1% of patients who achieved CRc at the RP2D remained on treatment or in post-SCT follow-up; patients on treatment continued to show evidence of evolving responses.

[0282] Zitomenib 600 mg continued to demonstrate significant clinical activity in heavily pretreated patients with co-mutated R / R NPM1-mAML. The safety profile was consistent with previous reports, and the on-target effect of DS remained manageable. Data showed that responses persisted with continued maturation of DoR, with 5 of 8 patients achieving CRc (4 of 7 at 600 mg and 1 CR at 200 mg), which is ongoing at the cutoff. A single-arm, registration-directed, Phase 2 study is currently underway to further evaluate zitomenib as a monotherapy in R / R NPM1-m AML.

[0283] Supplement 2. This report provides an update on the status of patients with NPM1-m in Phase 1a and Phase 1b, focusing on patients dosed with a 600 mg RP2D as of April 12, 2023 (N=20). The median age of patients receiving the 600 mg RP2D was 70.5 years (range, 22 to 86 years). FLT3 (30%) and IDH1 / 2 (40%) co-mutations were common (20% had both co-mutations). The median number of prior therapies was 3.0 (range, 1 to 10); 20% had received ≥1 prior stem cell transplant (SCT). Baseline characteristics of patients in Phase 1B are shown in Table 11.

[0284] Table 11.

[0285]

[0286]

[0287] Note: Data cutoff: April 12, 2023. a Patients can have both FLT3 and IDH1 / 2 and can be counted in both co-mutation categories. Other reasons for treatment discontinuation included physician decision, receipt of alternative anticancer treatment, subject withdrawal, and others. b All adverse events leading to discontinuation were not considered related to study drug. c Other reasons for study discontinuation included subject withdrawal and study completion. ECOG, Eastern Cooperative Oncology Group; FLT3, fms-like tyrosine kinase 3; IDH, isocitrate dehydrogenase; PS, performance score; SCT, stem cell transplantation.

[0288] According to the updated results, the complete remission (CR) rate of NPM1-m patients at 600 mg was 35%, of which 40% of patients achieved a composite CR (CRc) overall and the ORR was 45%. The median time to first response was 51 days (r: 26 to 225). The duration of one CR at the 200 mg dose was 35 cycles. According to Kaplan-Meier estimates, the median DoR for all NPM1-m patients who achieved CRc was 8.2 months (95% CI: 1.0 to NE). Two patients (1 CR and 1 CRi) underwent SCT and were still in remission at the end of the study, and one received maintenance therapy with zolpidem after SCT. The median duration of remission was 8.2 months.

[0289] Molecular analysis showed that zitomenib can achieve the elimination of measurable residual disease (MRD) of target mutations (such as NPM1) and co-mutations (such as FLT3 and IDH1), which may be achieved by targeting the initiating clones and subclonal events or by targeting aberrant gene expression, as at least two patients with FLT3 and IDH1 co-mutations at baseline became undetectable after two cycles. The data are shown in Table 12.

[0290] Table 12.

[0291]

[0292] Note: a Complete remission was defined as <5% bone marrow blasts with complete hematologic recovery and included CRmrd, CRmrd-, and CR without MRD assessment. b CR / CRh includes complete remission and CRh. c CRc was defined as achieving the best overall response among any of the following: CR (including CRmrd, CRmrd-, and CR without MRD assessment), CRh, CRi (including CRp). d Among patients with NPM1-m, 6 of 8 patients underwent MRD assessment; therefore, 66.7% of patients were MRD-negative. The MRD-negative rate was based on the number of patients who achieved CRc, ORR, complete remission, or CR / CRh. e Overall response was defined as achieving the best overall response among any of the following: MLFS, CRi (including CRp), CRh, CR (including CRmrd, CRmrd-, and CR without MRD assessment). The 95% CI was based on the Clopper-Pearson method. The efficacy set included all subjects from the mITT who had at least one post-baseline response assessment, or patients who died or discontinued the study before the first response assessment. CI, confidence interval; CR, complete remission; CRc, composite complete remission; CRh, complete remission with partial hematologic 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 intention-to-treat; MRD, measurable residual disease; MLFS, morphologic leukemia-free status; ORR, overall response rate; NPM1-m, nucleophosmin 1 mutation.

[0293] Most patients (85%) experienced at least one Grade 3 or higher treatment-emergent adverse event (TEAE); 30% were potentially treatment-related. The most common (>20%) Grade 3 or higher TEAEs were anemia (25%) and thrombocytopenia (20%). Differentiation syndrome (DS) of varying severity was reported in 20% of patients; the majority (n=3) were Grade 2.

[0294] The resistance profile was explored, and 1 of 29 patients (3.4%) was found to have the resistance mutation MEN1-M327I detected on C4D28; the patient's disease remained stable during cycle 7.

[0295] In summary, zitomenib demonstrated sustained and significant clinical activity in heavily pretreated patients with R / RNPM1-m AML harboring co-mutations, with 35% achieving a complete response (CR). The safety profile was consistent with previous reports, and DS flares were clinically manageable. Data demonstrated durable responses with MRD clearance for NPM1 and key co-mutations. The frequency of resistance mutations detected was low, and zitomenib demonstrated continued activity against common menin gatekeeper mutations.

[0296] Supplement 3. This report provides an update on the Phase 1 study of zitomenib in patients with AML as of August 30, 2023 (cutoff date). Patient demographics remain consistent with those reported in Table 11. No patients remained on treatment at cutoff, and four patients remained on study. Reasons for treatment discontinuation included adverse events (5 patients, 25%), death (1 patient, 5%), physician decision (1 patient, 5%), investigator-assessed disease progression (9 patients, 45%), receipt of alternative anticancer therapy (1 patient, 5%), and other (2 patients, 10%). Patients discontinued participation in the study due to study completion (1 patient, 5%) or death (15 patients, 75%).

[0297] In Phase 1a and 1b studies, 20 patients with relapsed / refractory NPM1-m AML (median 3 prior lines of therapy) received 600 mg of zitomenib daily. The complete remission (CR) rate at the cutoff date was 35% (95% confidence interval [CI], 15.4-59.2), the composite remission (CR / CRh) rate was 40%, and the overall response rate (ORR) was 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 a decrease in bone marrow blasts, cell count recovery, transfusion independence, and a negative test for measurable residual disease (MRD). The median overall survival of the 20 NPM1-m patients who received 600 mg was 5.6 months, and 12.1 months for CR / CRh responders.

[0298] Among 29 (3.4%) treated patients, 1 (12 or 31) had a known menin resistance mutation, MEN1-M327I, detected by RNA next-generation sequencing of serial bone marrow aspirates. No other resistance mutations were detected even in patients who had received at least two cycles of zolpidem and persisted with a measurable leukemia burden, suggesting that disease progression in these patients was not due to MEN1 mutations. In contrast, 39% (12 or 31) of patients who received at least two cycles of revumenib were found to have one or more MEN1 mutations, which often occurred concurrently with clinical progression (Perner et al., MEN1 mutations mediate clinical resistance to menin inhibition, Nature 2023, 615, 913-919).

[0299] Among all NPM1-m patients in phase 1a and 1b, the median duration of response was 51 days (range, 26-225). In phase 1a and 1b, the median duration of response for all NPM1-m patients who achieved a composite CR was 7.7 months, with a median follow-up duration of 13.4 months. One patient who achieved a CR at the 200 mg dose maintained remission for 35 cycles. Two patients (1 CR and 1 CRh) went on to undergo stem cell transplantation and remained in remission as of the cutoff date, with one patient still receiving maintenance therapy with zolpidem after transplantation. The 200 mg dose produced a lower CR / CRh recovery rate (6.7%) and a lower overall response rate (13.3%) compared to the 600 mg dose.

[0300] No QTc prolongation attributable to zitomenib was detected in this patient population. No significant drug interactions were observed. In contrast, the incidence of QT prolongation, a treatment-related adverse event, was 53% in patients treated with the menin inhibitor revumenib (Issa et al., The menin inhibitor revumenib in KMT2A-rearrangedor NPM1-mutantleukaemia, Nature 2023, 615, 920-924). Cases of grade 3 or higher differentiation syndrome are rare and have been effectively controlled. In patients treated with 200mg or 600mg of zitomenib, the incidence of differentiation syndrome in NPM1-m patients (15%) was lower than that in KMT2A-r patients (41%). No clinically significant cytopenia was observed in patients who achieved CR or CRh in the study.

[0301] The tabular data are shown in Tables 13 and 14.

[0302] Table 13.

[0303]

[0304] a CRc includes CR, CRh, CRi (including CRp), and MLFS; bOverall response rate includes CRc and MLFS; cTransfusion independence is defined as at least 56 consecutive days without a transfusion after baseline. The baseline period is defined as the period + / - 28 days from the first dose.

[0305] 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 hematologic recovery; CRp, complete remission with incomplete platelet recovery; HSCT, hematopoietic stem cell transplantation; KMT2Ar, lysine [K]-specific methyltransferase 2 rearrangement; MLFS, morphologic leukemia-free status; MRD, measurable residual disease; n, number; neg, negative; NE, not evaluable; NPM1 mutant, nucleolar phospholipid protein 1; OS, overall survival; PD, progressive disease; RBC, red blood cell; SD, stable disease.

[0306] Table 14.

[0307]

[0308] G. Summary

[0309] In summary, zitomenib demonstrated safety and tolerability. Reported adverse events were mostly consistent with the characteristics and manifestations of the underlying disease. No evidence of drug-induced QTc prolongation was observed. Differentiation syndrome, an on-target effect, was managed with monitoring and / or intervention for remission. Clinical activity of zitomenib monotherapy was found to be optimal at the 600 mg dose. NPM1-m achieved a good benefit / risk balance, with significant activity and a 30% CR rate (n=20), which increased to 35% over the course of the trial, a 35% CR / CRh rate, which increased to 40% over the course of the trial, and an ORR of 40%, which increased to 45% over the course of the trial. The high tissue penetration level of zitomenib may help clear extramedullary disease in patients with AML. For any genetic subgroup, increased exposure beyond 600 mg was not significantly associated with an increased probability of clinical response, and in particular, for NPM1-m subjects, increased exposure was not associated with an increased risk of grade ≥3 AEs (i.e., increased exposure did not increase safety risks). While early data from the trial focused on the 200mg dose, the expanded data set combined with pharmacokinetic analysis showed that the 600mg dose was superior to the 200mg dose in providing peak exposure without a significant increase in the risk of grade ≥3 adverse events. Specifically, for the NPM1-m patient population, the 600mg QD dose was superior to the 200mg dose.

[0310] A dose of 600 mg once daily was identified as the optimal biologic dose and was approved by the FDA as the recommended Phase 2 dose for further studies of zitomenib in the NPM1-m AML population.

[0311] Although both NPM1-m and KMT2A-r AML are menin-dependent, it can be assumed that the same dosing regimen is the optimal safe and effective dose for both groups. In fact, despite encouraging efficacy data in the combined population, the safety profile resulted in differences in response rates and benefit-risk between the two genotypes, possibly because of the more extensive extramedullary disease in the KMT2A-r subtype.

[0312] In Phase 1a, significant overlap in exposure was observed between the 200 mg and 400 mg dose levels, as well as between the 400 mg and 600 mg dose levels, suggesting similar clinical efficacy across all dose levels. Nevertheless, in the Phase 1a / 1b combination, clinically meaningful differences in response rates were observed in patients with NPM1-m: a CR rate of 16.7% with 200 mg and a rapid and durable CR rate of 35% with 600 mg. Treatment effects associated with CR included rapid recovery of hematologic parameters, which facilitated transfusion independence.

[0313] The safety profile of zitomenib in both genotype combinations was influenced by the experience of KMT2A-r patients and differed from the safety profile observed in NPM1-m patients. Specifically for differentiation syndrome, 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. Furthermore, cases of DS in NPM1-m patients were associated with clinical dysregulation, occurring in three of the four NPM1-m patients who experienced DS. The severity of DS in KMT2A-r patients may be related to the extensive extramedullary disease that is unique to this genotype.

[0314] H. Drug-resistant mutation studies

[0315] A variety of somatic resistance mutations in the MEN1 gene have been reported following treatment with menin inhibitors, including MEN1-M327I, MEN1-T349M, MEN1-G331R, and MEN1-G331D. For example, in another recent clinical trial of a menin inhibitor, the T349 mutation was detected in the majority of patients who acquired a menin gatekeeper mutation (Perner, F., Stein, EM, Wenge, DV, et al., MEN1 mutations mediate clinical resistance to menin inhibition. Nature 615, 913–919 (2023)). In the Phase 1 trial of zitomenib described here, mutational analysis (RNA sequencing) of clinical samples after zitomenib treatment revealed that one of the 29 patients tested (3.4%) developed a resistance mutation, MEN1-M327I. A mutation was detected in one patient at C4D28, but the patient maintained stable disease at cycle 7. It was reported that although the binding of zitomenib to the M327I mutant MEN1 was reduced relative to the wild-type protein in the menin-MLL binding assay, the IC of zitomenib for the T349M variant was 50 The binding activity remained below 100 nM. The data are shown in Table 15 (Grembecka, Development of new targeted therapeutics for AML, reported at the 3rd Biennial Miami Leukemia Symposium, March 31-April 2, 2023).

[0316] Table 15.

[0317] Menin form <![CDATA[IC of Zitomeni 50 (nM)]]> wild type 4.1 M327I 71 T349M 4.4 G331D ～2000

[0318] In summary, based on the data available so far, resistance mutations appear to occur rarely after treatment with zitomenib, and zitomenib retains binding activity against common menin gatekeeper mutations observed after exposure to menin inhibitors.

[0319] Thus, provided herein is a method of inhibiting the MEN1-MLL interaction, comprising contacting MEN1 with zitomenib, wherein MEN1 comprises a resistance mutation, wherein the resistance mutation is optionally selected from mutations at M327, T349, S160, and G331, and combinations thereof, and 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, leukemic cells, or AML comprises a MEN1 comprising a resistance mutation, optionally wherein the resistance mutation is optionally selected from mutations at M327, T349, S160, and G331, and combinations thereof, and wherein the mutation is optionally selected from M327I, M327V, T349M, S160T, G331R, and G331D, and combinations thereof. In some embodiments, the mutation is T349M or G331D. In some embodiments, the MEN1 resistance mutation is a de novo mutation. In some embodiments, the MEN1 resistance mutation is an acquired mutation, eg, developed after exposure to a menin inhibitor.

[0320] Although some embodiments of the present invention have been shown and described herein, it will be understood by those skilled in the art that these embodiments are provided by way of example only. The present invention is not intended to be limited by the specific examples provided in the specification. Although the present invention has been described with reference to the foregoing description, the description and illustration of the embodiments herein are not intended to be understood in a restrictive sense. Many variations, changes and substitutions can now be conceived by those skilled in the art without departing from the present invention. In addition, it will be understood that all aspects of the present invention are not limited to the specific description, configuration or relative proportions herein, which depend on various conditions and variables. It will be understood that in practicing the present invention, various alternatives to the embodiments of the present invention described herein may be adopted. Therefore, the present invention also encompasses any such alternatives, modifications, variations or equivalents. The following claims are intended to define the scope of the present invention and encompass methods and structures within the scope of these claims and their equivalents.

Claims

1. A method for treating acute leukemia in a subject, or a method for inhibiting proliferation of leukemia cells and / or inducing apoptosis of leukemia cells in a subject, comprising administering 600 mg of zitomenib or a pharmaceutically acceptable form thereof daily to the subject.

2. A method for treating extramedullary leukemia in an acute leukemic individual, comprising administering to said individual an effective amount of a menin inhibitor, particularly 600 mg of zitomenib or a pharmaceutically acceptable form thereof daily.

3. The method of claim 1 or claim 2, wherein the acute leukemia or leukemia cells are menin-dependent.

4. The method of any one of claims 1 to 3, wherein the acute leukemia or leukemia cell comprises a mutation selected from 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, optionally wherein 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.

5. The method of any one of claims 1 to 4, wherein the acute leukemia or leukemia cells comprise 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.

6. The method of any one of claims 1 to 5, wherein the acute leukemia is acute myeloid leukemia (AML), optionally wherein the AML is refractory AML, relapsed AML, or both relapsed and refractory AML, and optionally wherein the AML is acute promyelocytic leukemia, acute myeloblastic leukemia, or acute megakaryocytic leukemia.

7. The method of any one of claims 1 to 6, wherein the leukemia cells, acute leukemia or AML comprise an NPM1 mutation.

8. The method of any one of claims 1 to 6, wherein the leukemia cells, acute leukemia or AML comprise a KMT2A rearrangement.

9. The method of any one of claims 1 to 6, wherein the acute leukemia is acute lymphoblastic leukemia (ALL), optionally wherein the ALL is refractory ALL, relapsed ALL, or both relapsed and refractory ALL, and optionally wherein the ALL is precursor B acute lymphoblastic leukemia, precursor T acute lymphoblastic leukemia, Burkitt's leukemia, or acute biphenotypic leukemia.

10. The method of claim 9, wherein the ALL comprises an NPM1 mutation.

11. The method of claim 9, wherein the ALL comprises a KMT2A rearrangement.

12. The method of any one of claims 1 to 11, wherein administering zitomenib or a pharmaceutically acceptable form thereof comprises administering zitomenib or a pharmaceutically acceptable form thereof to the individual daily for at least 3 days, or at least 5 days, or at least 7 days, or at least 10 days, or at least 14 days, or at least 21 days, or at least 28 days, or a period of at least 28 days, or a period of 28 days.

13. The method of claim 12, wherein the administering comprises administering zitomenib or a pharmaceutically acceptable form thereof to the individual daily for N cycles, wherein a cycle comprises 28 days, and N is at least 1.

14. The method of claim 13, wherein N is 2, 3, 4, 5 or 6, or is at least 2, at least 3, at least 4, at least 5 or at least 6.

15. A method according to claim 13 or claim 14, wherein the N cycles are consecutive (ie there are 0 days between cycles).

16. The method of any one of claims 1 to 15, wherein following said administering, the subject has a risk of experiencing any Grade 3 or higher treatment-emergent adverse event (TEAE), regardless of causality, of less than about 80%, or less than about 75%, or about 71%.

17. The method of any one of claims 1 to 15, wherein following said administration, the risk of said subject experiencing any serious adverse event, regardless of causality, is less than about 65%, or less than about 60%, or less than about 55%, or about 53%.

18. The method of any one of claims 1 to 15, wherein following said administering, said subject has a risk of experiencing any differentiation syndrome suspected adverse event of 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 about 47%.

19. The method of any one of claims 1 to 17, wherein following said administering, said individual's risk of developing differentiation syndrome is less than about 25%, or less than about 20%, or less than about 19%, or less than about 18%, or about 18%.

20. The method of claim 19, wherein the probability that the differentiation syndrome comprises severe differentiation syndrome is less than about 50%, or less than about 45%, or less than about 40%, or less than about 35%, or about 33%.

21. The method of any one of claims 1 to 17, wherein following said administering, said individual's risk of 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 about 6%.

22. The method of any one of claims 1 to 17, wherein following said administering, said individual develops differentiation syndrome, and the probability that said differentiation syndrome developed in said individual is not severe differentiation syndrome (e.g., Grade 1 or Grade 2) is greater than about 50%, or greater than about 55%, or greater than about 60%, or greater than about 65%, or about 67%.

23. The method of any one of claims 1 to 22, wherein the administration results in a CR or CR / CRh rate of 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 about 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, or 35%, or about 35%.

24. The method of any one of claims 1 to 23, wherein the administration produces a CRc rate of 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 about 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39% or 40%.

25. The method of any one of claims 1 to 24, wherein the administration results in an ORR of 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 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%.

26. The method of any one of claims 7 or 12 to 25, wherein the administration results in a duration of remission (DoR) in individuals who achieve CRc of 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, or at least about 8.2 months, or about 8.2 months.

27. The method of any one of claims 1 to 26, wherein the individual develops differentiation syndrome, optionally wherein the differentiation syndrome is severe differentiation syndrome (e.g., Grade 3, Grade 4, or Grade 5), and has a probability of achieving an ORR of at least about 60%, or at least about 65%, or at least about 70%, or at least about 75%, or about 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, or 75%.

28. The method of any one of claims 1 to 27, wherein the acute leukemia or leukemia cell comprises an NPM1 mutation comprising a type A, type B, type C, or type D mutation.

29. The method of any one of claims 1 to 27, wherein the acute leukemia or leukemic cells comprise an NPM1 mutation comprising an insertion (eg, a 4-nucleotide insertion) in exon 12 of the NPM1 gene.

30. A method of increasing the level of myeloid blasts in the blood of an individual with AML, comprising administering to said individual an effective amount of a menin inhibitor, particularly 600 mg per day of zitomenib or a pharmaceutically acceptable form thereof.

31. The method of claim 30, wherein the AML is menin-dependent.

32. The method of claim 30 or claim 31 , wherein the AML comprises a mutation selected from 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, optionally wherein 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.

33. The method of any one of claims 30 to 32, wherein the AML comprises an NPM1 mutation, a KMT2A rearrangement, a SETD2 mutation, or a RUNX1 mutation.

34. The method of claim 33, wherein the AML comprises an NPM1 mutation or a KMT2A rearrangement, preferably wherein the AML comprises an NPM1 mutation.

35. The method of claim 33 or claim 34, wherein the relative level of myeloid progenitor cells in the blood of the individual is assessed by analyzing two time-spaced blood samples from the individual, optionally wherein the blood samples are collected at, e.g., (a) a first time point and a second time point, wherein both time points are during the administration, or (b) a first time point before the start of the administration and a second time point during the administration (e.g., wherein the first time point is before Cycle 1, Day 1 and the second time point is at least 7, 14, 21 or 28 days later, such as a day from Cycle 1, Day 2 to Cycle 1, Day 28).

36. The method of claim 35, wherein each analysis is a complete blood count (CBC), optionally with differential.

37. The method of claim 35 or 36, wherein the first time point and the second time point 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 time point is at a time when the individual achieves complete remission (CR).

38. The method of any one of claims 33 to 37, wherein an increase in the level of myeloid blasts in the individual's blood is not associated with progression of the AML.

39. The method of any one of claims 33 to 38, wherein the increase in the level of myeloid blasts occurs in the extramedullary space.

40. The method according to claim 39, wherein said increase in the level of myeloid blasts indicates that said individual is sensitive to said menin inhibitor, in particular zitomenib or a pharmaceutical form thereof.

41. A method of identifying an individual whose acute leukemia (particularly AML) is sensitive to administration of a menin inhibitor (particularly zitomenib), comprising: administering to the individual an effective amount of the menin inhibitor, particularly 600 mg of zitomenib or a pharmaceutically acceptable form thereof per day; obtaining, at a first time point before the start of the administering or during the administering, an identification result of the level of myeloid blasts in a first blood sample collected from the individual; obtaining, at a second time point after the first time point and during the administration, an identification of the level of myeloid blasts in a second blood sample collected from the individual; as well as If the level of myeloid blasts at the second time point is higher than the level at the first time point, the acute leukemia is determined to be sensitive to the administration.

42. A method of treating a differentiation disorder, particularly tumor lysis syndrome, in a subject diagnosed with an acute leukemia, or reducing the risk of developing a severe differentiation disorder in a subject with an acute leukemia, optionally wherein the acute leukemia comprises: (a) administering to the individual an effective amount of a menin inhibitor, in particular 600 mg of zitomenib or a pharmaceutically acceptable form thereof per day; (b) administering IV rehydration to the individual, and optionally, (c) administering to said individual an effective amount of a xanthine oxidase inhibitor, optionally wherein said xanthine oxidase inhibitor is allopurinol, optionally administering said allopurinol at a dose of about 200-400 mg / m2 / day in 1-3 divided doses, up to a maximum of about 800 mg daily.

43. The method of claim 42, comprising administering the xanthine oxidase inhibitor, and comprising, prior to administering the xanthine oxidase inhibitor, diagnosing the individual as having a low risk or an intermediate risk of having or developing the differentiation disorder by obtaining the following identification in the individual: (1) White blood cell count is less than about 25×10 9 / L and lactate dehydrogenase level is less than twice the upper limit of normal, or (2) White blood cell count is about 25 to about 100×10 9 / L, or (3) White blood cell count is less than about 25×10 9 / L, and lactate dehydrogenase level is more than twice the upper limit of normal.

44. A method of treating a differentiation disorder in a subject with acute leukemia or reducing the risk of a subject with acute leukemia developing a severe differentiation disorder, comprising: (a) administering to the individual an effective amount of a menin inhibitor, in particular 600 mg of zitomenib or a pharmaceutically acceptable form thereof per day; (b) administering IV rehydration 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.

45. The method of claim 44, comprising, prior to administering the rasburicase, diagnosing the individual as having a high risk of having or developing the differentiation disorder by obtaining the following identification in the individual: (i) having a white blood cell count level greater than or equal to about 100×10 9 / L, or (ii) having a white blood cell count level (i) of about 25 to about 100×10 9 / L, or (ii) less than about 25×10 9 / L and lactate dehydrogenase level is greater than twice the upper limit of normal, and For each of (i) and (ii), wherein the individual has renal insufficiency, or uric acid, potassium, and / or phosphate levels above the applicable upper limit of normal.

46. A method of treating a differentiation disorder in an individual with acute leukemia or reducing the risk of developing a severe differentiation disorder, comprising: (a) administering to the individual a prophylactic and / or effective amount of a corticosteroid, 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 to the individual a therapeutically effective amount of a menin inhibitor.

47. The method of claim 46, wherein the corticosteroid and the menin inhibitor are administered daily, and are administered consecutively or simultaneously, optionally comprising administering the first dose of the corticosteroid and the menin inhibitor, respectively, on or about the same day, or administering the first dose of the corticosteroid on a day before or after the first administration of the menin inhibitor.

48. The method according to claim 46 or 47, wherein Prior to administration of the corticosteroid or the menin inhibitor, the individual has one or more of the following: a white blood cell count greater than about 5×10 9 / L, increased serum creatinine level, severe extramedullary disease, and hyperplastic acute leukemia.

49. The method of any one of claims 46 to 48, comprising administering the corticosteroid daily starting on day one, administering the menin inhibitor daily starting on the same day or a subsequent day, and reducing the dose of the corticosteroid after about 28 days of administering the menin inhibitor if the individual has not been 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 improves and the level of bone marrow blasts is less than about 5% (in the method of reducing the risk or the method of treatment).

50. The method of any one of claims 46 to 48, comprising administering to the subject intravenously a dose of dexamethasone (or an equivalent dose of an alternative oral or IV corticosteroid) of about 5 mg, 10 mg, or 15 mg, or about 5 to 10 mg, preferably about 10 mg, every 12 hours for one, two, or three days.

51. The method of any one of claims 46 to 50, comprising: if the white blood cell count or leukocyte count of the subject increases to greater than about 10 x 10 9 / L or doubled, administering to the individual a therapeutically effective amount of hydroxyurea, and optionally, administering to the individual a therapeutically effective amount of cytarabine, idarubicin, or gemtuzumab.

52. The method of claim 51, comprising gradually reducing the dosage and / or ceasing the administration of the corticosteroid, hydroxyurea, cytarabine, idarubicin, or gemtuzumab after improvement of the differentiation disorder.

53. The method of any one of claims 46 to 52, comprising interrupting said administration of said menin inhibitor during all or part of said administration of one or more of IV rehydration, allopurinol, rasburicase, prednisone, dexamethasone, hydroxyurea, cytarabine, idarubicin, and gemtuzumab, and interrupting said administration of said menin inhibitor after said differentiation disorder has improved (e.g., when said white blood cell count has dropped to less than about 20×10 9 / L) restart the administration of the therapeutically effective dose or a reduced dose of the menin inhibitor.

54. The method of any one of claims 42 to 53, wherein the differentiation disorder is differentiation syndrome with or without leukocytosis or tumor lysis syndrome.

55. The method of any one of claims 41 to 54, wherein the acute leukemia comprises AML.

56. The method of any one of claims 41 to 54, wherein the acute leukemia comprises ALL.

57. The method of claim 55 or claim 56, wherein the acute leukemia comprises an NPM1 mutation.

58. The method of any one of claims 1 to 57, wherein the individual is ≥ 18 years old.

59. The method of any one of claims 41 to 58, wherein the menin inhibitor is zitomenib or a pharmaceutically acceptable form thereof.

60. The method of any one of claims 1 to 59, wherein daily administration is once daily administration.

61. The method according to any one of claims 1 to 60, wherein the zitomenib or a pharmaceutically acceptable salt thereof is zitomenib or a pharmaceutically acceptable salt thereof, or a solvate thereof, optionally zitomenib free base or a solvate thereof.

62. The method of any one of claims 1 to 61, wherein the 600 mg zitomenib or a pharmaceutically acceptable form thereof is an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or a submaximal tolerated dose of zitomenib or a pharmaceutically acceptable form thereof.

63. The method of any one of claims 41 to 62, wherein the acute leukemia is menin-dependent.

64. The method of any one of claims 41 to 63, wherein the acute leukemia comprises a mutation selected from 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.

65. The method according to any one of claims 41 to 64, 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.

66. A pharmaceutical composition comprising an optimal biological dose, a recommended Phase 2 dose, a safe and effective dose, or a submaximal tolerated dose of zitomenib or a pharmaceutically acceptable form thereof, and a pharmaceutically acceptable carrier.

67. The pharmaceutical composition of claim 66, wherein the optimal biological dose, the recommended Phase 2 dose, the safe and effective dose, or the submaximal tolerated dose is 600 mg.

68. The pharmaceutical composition of claim 66 or claim 67, wherein the zitomenib or a pharmaceutically acceptable form thereof has Breakthrough Therapy designation.

69. The pharmaceutical composition of any one of claims 66 to 68, wherein the pharmaceutical composition comprises one or more dosage forms, such as one or more oral dosage forms, optionally wherein each oral dosage form comprises 50 to 600 mg of zitomenib, or optionally wherein each oral dosage form comprises 50 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg or 600 mg of zitomenib, wherein the total zitomenib in the one or more oral dosage forms is 600 mg.

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