EP4648756A1 - Anti-cancer action of n-alkylated anthracycline derivatives in cancers, including glioblastoma and pediatric diffuse midline glioma - Google Patents
Anti-cancer action of n-alkylated anthracycline derivatives in cancers, including glioblastoma and pediatric diffuse midline gliomaInfo
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- EP4648756A1 EP4648756A1 EP24741872.6A EP24741872A EP4648756A1 EP 4648756 A1 EP4648756 A1 EP 4648756A1 EP 24741872 A EP24741872 A EP 24741872A EP 4648756 A1 EP4648756 A1 EP 4648756A1
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- European Patent Office
- Prior art keywords
- cancer
- compound
- tumor
- cell
- melanoma
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/335—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin
- A61K31/365—Lactones
- A61K31/366—Lactones having six-membered rings, e.g. delta-lactones
Definitions
- ANTI-CANCER ACTION OF N-ALKYLATED ANTHRACYCLINE DERIVATIVES IN CANCERS INCLUDING GLIOBLASTOMA AND PEDIATRIC DIFFUSE MIDLINE GLIOMA BACKGROUND
- Doxorubicin for instance, is prescribed to over 1 million patients worldwide for the treatment of various hematologic and solid tumors. These drugs, however, to date have had limited success in treating brain tumors, such as glioblastomas and diffuse midline glioma.
- the presently disclosed subject matter provides a compound of formula (I): (I); wherein: X is H C1-C8 alkyl; R 3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof.
- the compound of formula (I) is selected from: O 02 O OH O OH .
- disclosed subject matter provides a pharmaceutical formulation comprising the compound of formula (I) and a pharmaceutically acceptable carrier.
- the presently disclosed subject matter provides a method for treating a cancer in a subject in need of treatment thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of formula (I).
- the cancer is associate with an oncogenic histone H3 mutation.
- the cancer is selected from adrenocortical carcinoma, salivary gland cancer, B-lymphoblastic leukemia/lymphoma, leukemia, ampullary cancer, bladder cancer, breast cancer, renal cell carcinoma, cervical cancer, hepatobiliary cancer, cholangiocarcinoma, mature B-cell neoplasms, colorectal cancer, skin cancer, non-melanoma, mature T and NK neoplasms, melanoma, esophagogastric cancer, bone cancer, glioblastoma, head and neck cancer, renal non-clear cell carcinoma, renal clear cell carcinoma, glioma, non-small cell lung cancer, embryonal tumor, pleural mesothelioma, prostate cancer, gastrointestinal neuroendocrine tumor, cancer of unknown primary, pancreatic cancer, endometrial cancer, thymic tumor, soft tissue sarcoma, small cell lung cancer, penile cancer, gastrointestinal stromal tumor, ovarian
- the cancer is associated with an oncogenic histone H3 lysine 27 to methionine (K27M) mutation.
- the cancer is selected from diffuse intrinsic pontine glioma, diffuse midline glioma, and glioblastoma. 2 41278.601_P17027-02
- the cancer is associated with an alteration in H3K27me regulators.
- the cancer is associated with an overexpression of EZH2.
- the cancer is selected from chronic lymphocytic leukemia, myelodysplastic syndrome, acute myeloid leukemia, natural killer/T-cell lymphoma, melanoma, endometrial, prostate, and breast cancer, and neuroblastoma.
- the cancer is associated with an Ezh2 mutation (H3K27me3 methyltransferase).
- the cancer is selected from non-Hodgkin’s lymphoma, T-cell acute lymphoblastic leukemia, myeloproliferative disorders, myeloid leukemia, melanoma, head and neck squamous cell carcinoma, and malignant peripheral nerve sheath tumors.
- the cancer is associated with a mutation in Polycomb group- associated proteins (H3K27me3 methyltransferase complex).
- the cancer is selected from a myeloid leukemia, glioblastoma, non-Hodgkin’s lymphoma, bladder cancer, pancreatic cancer, and multiple myeloma.
- the cancer is associated with oncogenic deregulation of histone H3 K27me3 modification and Ezh2 activity.
- the cancer is small cell lung cancer or non-small cell lung cancer.
- the subject is a pediatric patient.
- FIG. 1A and FIG. 1B show: (FIG.
- FIG. 1A In H3-K27M mutant diffuse midline glioma (DMG), incorporation of onco-histones into chromatin leads to altered epigenetic regulation and gene expression changes;
- FIG. 1B Without wishing to be bound to any one particular theory, it is thought that aclarubicin can specifically evict H3-K27M mutant histones from chromatin as a novel therapeutic strategy for DMG;
- FIG. 3A and FIG. 3B show the differential expression of H3-K27M dependent genes following aclarubicin treatment in JHH-DIPG-1 cells.
- FIG. 3A is a volcano plot: aclarubicin vs. DMSO treatment.
- FIG. 3B shows differential expression of K27M-dependent genes following Aclarubicin treatment;
- FIG. 4 shows gene set enrichment in down-regulated genes;
- FIG. 5 shows MYC expression with HSJD-DIPG-007 cells;
- FIG. 6 shows pseudo-bulk sc-ATAC-seq analysis;
- FIG. 7 is an RNA-seq:PCA plot with SF7761 cells;
- FIG. 8 is HSJD DIPG 007:NND vs. Dauno. Top GSEA enrichment among upregulated genes.
- FIG. 9 is HSJD DIPG 007.
- FIG. 10 is dose-response viability assays of patient-derived diffuse midline glioma cell lines treated with compound 5
- FIG. 11 shows the simultaneous downregulation of oncogenic drivers of diffuse midline glioma by compound 5.
- Patient-derived DMG neurosphere cell line HSJD-DIPG- 007 was treated with DMSO control or indicated concentrations of compound 5 for 24 hours. Western blotting for indicated protein targets was performed.
- GAPDH is used as a protein loading control.
- DMG DMG-derived neurotrophic factor-like receptor-like receptor
- c-Myc c-Myc
- Olig2 EGFR
- Cell line JHH-DIPG-1 was 4 41278.601_P17027-02 treated with DMSO control, aclarubicin (Acla), daunorubicin (Dauno), or compound 5 at the 250 nM, 500 nM, or 1 ⁇ M, as indicated, for 24 hours, and Western blotting for indicated protein targets was performed.
- GAPDH is used as a protein loading control.
- Phospho- H2AX is a marker of the double-strand DNA break response.
- FIG. 13a, FIG. 13b, FIG. 13c, FIG. 13d, FIG. 13e, FIG. 13f, FIG. 13g, FIG. 13h, FIG. 13i, FIG. 13j, FIG. 13k, FIG. 13l, FIG. 13m, and FIG. 13n show IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines.
- N-alkylated anthracycline derivatives of Formula (I) N-alkylated anthracycline derivatives of Formula (I)
- the presently disclosed subject matter provides a compound of formula (I): 5 41278.601_P17027-02 I); wherein: X is H y C 1 -C 8 alkyl; R 3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof.
- C1-C8 alkyl includes methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, sec-pentyl, isopentyl, neopentyl, n-hexyl, sec-hexyl, n-heptyl, and n-octyl.
- the compound of formula (I) is selected from: O OH O blood-brain barrier penetration and exhibit specific gene expression effect (downregulates aberrantly expressed onco-histone targets, induces differentiation, and the like).
- the presently disclosed subject matter provides a method for treating a cancer in a subject in need of treatment thereof, the method comprising 6 41278.601_P17027-02 administering to the subject a therapeutically effective amount of a compound of formula (I):. ; wherein: X is H or C1-C8 alkyl; R 3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof.
- the compound of formula (I) is selected from: O OH O
- the presently disclosed compounds in some embodiments, can be used to treat primary brain cancers, brain metastases of other solid tumors, and hematologic malignancies.
- histone H3 K27 methylation Alterations of histone H3 K27 methylation are observed in a wide range of cancers, which may be targeted by these compounds.
- the general relevance of histone H3 K27me alterations across a wide variety of cancer types has been the subjected of multiple in-depth scientific reviews. See Nichol et al., 2016; Shen and Laird, 2013.
- the presently disclosed compounds can be used to treat cancers with oncogenic Histone H3 mutations including, but not limited to histone mutations in human tumors selected from adrenocortical carcinoma, salivary gland cancer, B- lymphoblastic leukemia/lymphoma, leukemia, ampullary cancer, bladder cancer, breast cancer, renal cell carcinoma, cervical cancer, hepatobiliary cancer, cholangiocarcinoma, mature B-cell neoplasms, colorectal cancer, skin cancer, non-melanoma, mature T and NK neoplasms, melanoma, esophagogastric cancer, bone cancer, glioblastoma, head and neck cancer, renal non-clear cell carcinoma, renal clear cell carcinoma, glioma, non-small cell lung cancer, embryonal tumor, pleural mesothelioma, prostate cancer, gastrointestinal neuroendocrine tumor, cancer of unknown primary
- the cancer is related to an oncogenic histone H3 lysine 27 to methionine (K27M) mutation in diffuse intrinsic pontine glioma, diffuse midline glioma, and glioblastoma.
- K27M histone H3 lysine 27 to methionine
- the presently disclosed compounds can be used to treat cancers with alterations in H3K27me regulators, including overexpression of EZH2 in chronic lymphocytic leukemia, myelodysplastic syndrome, acute myeloid leukemia, natural killer/T-cell lymphoma, melanoma, endometrial, prostate, and breast cancer, and neuroblastoma.
- the presently disclosed compounds can be used to treat cancers with Ezh2 mutations (H3K27me3 methyltransferase) including, but not limited to, non-Hodgkin’s lymphoma, T-cell acute lymphoblastic leukemia, myeloproliferative disorders, myeloid leukemia, melanoma, head and neck squamous cell carcinoma, and malignant peripheral nerve sheath tumors.
- Ezh2 mutations H3K27me3 methyltransferase
- non-Hodgkin’s lymphoma T-cell acute lymphoblastic leukemia, myeloproliferative disorders, myeloid leukemia, melanoma, head and neck squamous cell carcinoma, and malignant peripheral nerve sheath tumors.
- the presently disclosed compounds can be used to treat cancers with mutations in Polycomb group-associated proteins (H3K27me3 methyltransferase complex) including, but not limited to, myeloid leukemias, glioblastoma, non-Hodgkin’s lymphoma, bladder cancer, pancreatic cancer, and multiple myeloma.
- Polycomb group-associated proteins H3K27me3 methyltransferase complex
- the presently disclosed compounds can be used to treat cancers with oncogenic deregulation of histone H3 K27me3 modification and Ezh2 activity including, but not limited to, small cell lung cancer and non-small cell lung cancer. See Zhang et al., 2016. In particular embodiments, the subject is a pediatric patient.
- the term “treating” can include reversing, alleviating, inhibiting the progression of, preventing or reducing the likelihood of the disease, disorder, or condition to which such term applies, or one or more symptoms or manifestations of such disease, disorder or condition.
- Preventing refers to causing a disease, disorder, condition, or symptom or manifestation of such, or worsening of the severity of such, not to occur. Accordingly, the presently disclosed compounds can be administered prophylactically to prevent or reduce the incidence or recurrence of the disease, disorder, or condition.
- the “therapeutically effective amount” of an active agent or drug delivery device refers to the amount necessary to elicit the desired biological response. As will be appreciated by those of ordinary skill in this art, the effective amount of an agent or device may vary depending on such factors as the desired biological endpoint, the agent to be delivered, the makeup of the pharmaceutical composition, the target tissue, and the like.
- a “subject” treated by the presently disclosed methods in their many embodiments is desirably a human subject, although it is to be understood that the methods described herein are effective with respect to all vertebrate species, which are intended to be included in the term “subject.” Accordingly, a “subject” can include a human subject for medical purposes, such as for the treatment of an existing condition or disease or the prophylactic treatment for preventing the onset of a condition or disease, or an animal subject for medical, veterinary purposes, or developmental purposes.
- Suitable animal subjects include mammals including, but not limited to, primates, e.g., humans, monkeys, apes, and the like; bovines, e.g., cattle, oxen, and the like; ovines, e.g., sheep and the like; caprines, e.g., goats 9 41278.601_P17027-02 and the like; porcines, e.g., pigs, hogs, and the like; equines, e.g., horses, donkeys, zebras, and the like; poultry, such as domestic fowls including, but not limited to chickens, turkeys, geese, ducks, quail, guinea fowl, and pigeons; felines, including wild and domestic cats; canines, including dogs; lagomorphs, including rabbits, hares, and the like; and rodents, including mice, rats, and the like.
- mammals including, but not limited to
- an animal may be a transgenic animal.
- the subject is a human including, but not limited to, fetal, neonatal, infant, juvenile, and adult subjects.
- a “subject” can include a patient afflicted with or suspected of being afflicted with a condition or disease.
- the terms “subject” and “patient” are used interchangeably herein.
- the term “subject” also refers to an organism, tissue, cell, or collection of cells from a subject.
- the subject is a human subject.
- the subject is an adult subject.
- the subject is an infant or pediatric subject.
- the subject has an age selected from about 16 years of age or less, about 12 years of age or less, about 8 years of age or less, about 5 years of age or less, and about 2 years of age or less.
- the subject is a pediatric patient.
- the term “pediatric” refers to a patient aged 21 or younger at the time of their diagnosis or treatment. Pediatric subpopulations are further categorized as follows: neonates - from birth through the first 28 days of life; infants - 29 days to less than 2 years; children - 2 years to less than 12 years; and adolescents - aged 12 through 21 (up to but not including the 22nd birthday).
- the term “combination” is used in its broadest sense and means that a subject is administered at least two agents, more particularly a compound described herein and at least one other therapeutic agent. More particularly, the term “in combination” refers to the concomitant administration of two (or more) active agents for the treatment of a, e.g., single disease state.
- the active agents may be combined and administered in a single dosage form, may be administered as separate dosage forms at the same time, or may be administered as separate dosage forms that are administered alternately or sequentially on the same or separate days. In one embodiment of the presently disclosed subject matter, the active agents are combined and administered in a single dosage form.
- the active agents are administered in separate dosage forms (e.g., wherein it is 10 41278.601_P17027-02 desirable to vary the amount of one but not the other).
- the single dosage form may include additional active agents for the treatment of the disease state.
- the compositions described herein can be administered alone or in combination with adjuvants that enhance stability of the compositions, alone or in combination with one or more therapeutic agents, facilitate administration of pharmaceutical compositions containing them in certain embodiments, provide increased dissolution or dispersion, increase inhibitory activity, provide adjunct therapy, and the like, including other active ingredients.
- combination therapies utilize lower dosages of the conventional therapeutics, thus avoiding possible toxicity and adverse side effects incurred when those agents are used as monotherapies.
- a subject administered a combination of a compound described herein and at least one additional therapeutic agent can receive a compound and at least one additional therapeutic agent at the same time (i.e., simultaneously) or at different times (i.e., sequentially, in either order, on the same day or on different days), so long as the effect of the combination of both agents is achieved in the subject.
- agents administered sequentially can be administered within 1, 5, 10, 30, 60, 120, 180, 240 minutes or longer of one another. In other embodiments, agents administered sequentially, can be administered within 1, 5, 10, 15, 20 or more days of one another.
- the compound described herein and at least one additional therapeutic agent are administered simultaneously, they can be administered to the subject as separate pharmaceutical compositions, each comprising either a compound or at least one additional therapeutic agent, or they can be administered to a subject as a single pharmaceutical composition comprising both agents.
- the effective concentration of each of the agents to elicit a particular biological response may be less than the effective concentration of each agent when administered alone, thereby allowing a reduction in the dose of one or more of 11 41278.601_P17027-02 the agents relative to the dose that would be needed if the agent was administered as a single agent.
- the effects of multiple agents may, but need not be, additive or synergistic.
- the agents may be administered multiple times. In some embodiments, when administered in combination, the two or more agents can have a synergistic effect.
- the terms “synergy,” “synergistic,” “synergistically” and derivations thereof, such as in a “synergistic effect” or a “synergistic combination” or a “synergistic composition” refer to circumstances under which the biological activity of a combination of a compound described herein and at least one additional therapeutic agent is greater than the sum of the biological activities of the respective agents when administered individually.
- Synergy can be expressed in terms of a “Synergy Index (SI),” which generally can be determined by the method described by F. C.
- a “synergistic combination” has an activity higher that what can be expected based on the observed activities of the individual components when used alone.
- a “synergistically effective amount” of a component refers to the amount of the component necessary to elicit a synergistic effect in, for example, another therapeutic agent present in the composition.
- compositions include the pharmaceutically acceptable salts of the compounds described above.
- Pharmaceutically acceptable salts are generally well known to those of ordinary skill in the art, and include salts of active compounds which are prepared with relatively nontoxic acids or bases, depending on the particular substituent moieties found on the compounds described herein.
- base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent or by ion exchange, whereby one basic counterion (base) in an ionic complex is substituted for another.
- Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt.
- acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent or by ion exchange, whereby one acidic counterion (acid) in an ionic complex is substituted for another.
- Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p- toluenesulfonic, citric, tartaric, methanesulfonic, trifluoroacetic acid (TFA), and the like.
- inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric
- salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al, “Pharmaceutical Salts”, Journal of Pharmaceutical Science, 1977, 66, 1-19).
- Certain specific compounds of the present disclosure contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.
- salts suitable for use with the presently 13 41278.601_P17027-02 disclosed subject matter include, by way of example but not limitation, acetate, benzenesulfonate, benzoate, bicarbonate, bitartrate, bromide, calcium edetate, camsylate, carbonate, citrate, edetate, edisylate, estolate, esylate, fumarate, gluceptate, gluconate, glutamate, glycollylarsanilate, hexylresorcinate, hydrabamine, hydrobromide, hydrochloride, hydroxynaphthoate, iodide, isethionate, lactate, lactobionate, malate, maleate, mandelate, mesylate, mucate, napsylate, nitrate, pamoate (embonate), pantothenate, phosphate/diphosphate, polygalacturonate,
- compositions of the disclosure can be formulated for a variety of modes of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remington: The Science and Practice of Pharmacy (20 th ed.) Lippincott, Williams & Wilkins (2000). Depending on the specific conditions being treated, such agents may be formulated into liquid or solid dosage forms and administered systemically or locally. The agents may be delivered, for example, in a timed- or sustained-slow release form as is known to those skilled in the art.
- Suitable routes may include oral, buccal, by inhalation spray, sublingual, rectal, transdermal, vaginal, transmucosal, nasal or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intra-articullar, intra -sternal, intra-synovial, intra-hepatic, intralesional, intracranial, intraperitoneal, intranasal, or intraocular injections or other modes of delivery.
- the agents of the disclosure may be formulated and diluted in aqueous solutions, such as in physiologically compatible buffers such as Hank’s solution, Ringer’s solution, or physiological saline buffer.
- aqueous solutions such as in physiologically compatible buffers such as Hank’s solution, Ringer’s solution, or physiological saline buffer.
- penetrants appropriate to the barrier to be permeated are used in the formulation.
- penetrants are generally known in the art.
- Use of pharmaceutically acceptable inert carriers to formulate the compounds herein 14 41278.601_P17027-02 disclosed for the practice of the disclosure into dosages suitable for systemic administration is within the scope of the disclosure.
- the compositions of the present disclosure in particular, those formulated as solutions, may be administered parenterally, such as by intravenous injection.
- the compounds can be formulated readily using pharmaceutically acceptable carriers well known in the art into dosages suitable for oral administration.
- Such carriers enable the compounds of the disclosure to be formulated as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject (e.g., patient) to be treated.
- the agents of the disclosure also may be formulated by methods known to those of skill in the art, and may include, for example, but not limited to, examples of solubilizing, diluting, or dispersing substances, such as saline; preservatives, such as benzyl alcohol; absorption promoters; and fluorocarbons.
- the presently disclosed compounds are administered intranasally in a form selected from the group consisting of a nasal spray, a nasal drop, a powder, a granule, a cachet, a tablet, an aerosol, a paste, a cream, a gel, an ointment, a salve, a foam, a paste, a lotion, a cream, an oil suspension, an emulsion, a solution, a patch, and a stick.
- the term administrating via an "intranasal route” refers to administering by way of the nasal structures. It has been found that the presently disclosed compounds are much more effective at penetrating the brain when administered intranasally.
- Intranasal administration generally allows the active agent to bypass first pass metabolism, thereby enhancing the bioavailability of the active agent.
- Such delivery can offer several advantages over other modes of drug delivery, including, but not limited to, increasing the onset of action, lowering the required dosage, enhancing the efficacy, and improving the safety profile of the active agent.
- tablet dosage forms enter the bloodstream through the gastrointestinal tract, which subjects the drug to degradation from stomach acid, bile, digestive enzymes, and other first pass metabolism effects. As a result, tablet formulations often require higher doses and generally have a delayed onset of action.
- Nasal administration of a drug also can facilitate compliance, especially for pediatric patients, geriatric patients, patients suffering from a neurodegenerative disease, or other patients for which swallowing is difficult, e.g., patients suffering from nausea, such as 15 41278.601_P17027-02 patients undergoing chemotherapy, or patients with a swallowing disorder.
- Intranasal (“i.n.” or “IN”) delivery of an agent to a subject can facilitate delivery of the agent to the brain and/or peripheral nervous system.
- Such administration is non-invasive and offers several advantages including avoidance of hepatic first pass clearance, rapid onset of action, frequent self-administration and easy dose adjustments.
- compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically.
- the agents of the disclosure may be formulated by methods known to those of skill in the art, and may include, for example, but not limited to, examples of solubilizing, diluting, or dispersing substances, such as saline, preservatives, such as benzyl alcohol, absorption promoters, and fluorocarbons.
- Optimized formulations for intranasal delivery may include addition of permeability enhancers (mucoadhesives, nanoparticles, and the like) as well as combined use with an intranasal drug delivery device (for example, one that provides controlled particle dispersion with particles aerosolized to target the upper nasal cavity).
- polymer-based nanoparticles including chitosan, maltodextrin, polyethylene glycol (PEG), polylactic acid (PLA), polylactic-co-glycolic acid (PLGA), and PAMAM dendrimer; gels, including poloxamer; and lipid-based formulations, including glycerol monocaprate (CapmulTM), mixtures of mono-, di-, and triglycerides and mono- and di- fatty esters of PEG (LabrafilTM), palmitate, glycerol monostearate, and phospholipids can be used to administer the presently disclosed compounds intranasally.
- the presently disclosed compounds also can be administered intranasally via mucoadhesive agents.
- Mucoadhesion is commonly defined as the adhesion between two materials, at least one of which is a mucosal surface. More particularly, mucoadhesion is the interaction between a mucin surface and a synthetic or natural polymer. Mucoadhesive dosage forms can be designed to enable prolonged retention at the site of application, 16 41278.601_P17027-02 providing a controlled rate of drug release for improved therapeutic outcome. Application of dosage forms to mucosal surfaces may be of benefit to drug molecules not amenable to the oral route, such as those that undergo acid degradation or extensive first-pass metabolism.
- Mucoadhesive materials suitable for use with nasal administration of the presently disclosed compounds include, but are not limited to, soluble cellulose derivatives, such as hydroxypropyl methylcellulose (HPMC), hydroxypropyl cellulose (HPC), methylcellulose (MC), and carboxymethyl cellulose (CMC), and insoluble cellulose derivatives, such as ethylcellulose and microcrystalline cellulose (MCC), starch (e.g., Amioca ® ), polyacrylates, such as poly(acrylic acid) (e.g., Carbopol ® 974P), functionalized mucoadhesive polymers, such as polycarbophil, hyaluronan, and amberlite resin, and chitosan (2-amino-2-deoxy- (l ⁇ 4)- ⁇ -d-glucopyranan) formulations and derivatives thereof.
- HPMC hydroxypropyl methylcellulose
- HPC hydroxypropyl cellulose
- MC methylcellulose
- CMC carboxymethyl cellulose
- the formulation also includes a permeability enhancer.
- permeability enhancer refers to a substance that facilitates the delivery of a drug across mucosal tissue.
- the term encompasses chemical enhancers that, when applied to the mucosal tissue, render the tissue more permeable to the drug.
- Permeability enhancers include, but are not limited to, dimethyl sulfoxide (DMSO), hydrogen peroxide (H 2 O 2 ), propylene glycol, oleic acid, cetyl alcohol, benzalkonium chloride, sodium lauryl sulphate, isopropyl myristate, Tween 80, dimethyl formamide, dimethyl acetamide, sodium lauroylsarcosinate, sorbitan monolaurate, methylsulfonylmethane, Azone, terpenes, phosphatidylcholine dependent phospholipase C, triacyl glycerol hydrolase, acid phosphatase, phospholipase A2, concentrated saline solutions (e.g., PBS and NaCl), polysorbate 80, polysorbate 20, sodium dodecanoate (C12), sodium caprate (CIO) and/or sodium palmitate (CI 6), tert-butyl cyclohexanol (TBCH
- the intranasal administration is accomplished via a ViaNaseTM device (Kurve Technology, Inc.).
- Pharmaceutical compositions suitable for use in the present disclosure include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.
- the compounds according to the disclosure are effective over a wide dosage 17 41278.601_P17027-02 range.
- dosages from 0.01 to 1000 mg, from 0.5 to 100 mg, from 1 to 50 mg per day, and from 5 to 40 mg per day are examples of dosages that may be used.
- a non-limiting dosage is 10 to 30 mg per day.
- these pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically.
- suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically.
- the preparations formulated for oral administration may be in the form of tablets, dragees, capsules, or solutions.
- compositions for oral use can be obtained by combining the active compounds with solid excipients, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores.
- suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl- cellulose, sodium carboxymethyl-cellulose (CMC), and/or polyvinylpyrrolidone (PVP: povidone).
- disintegrating agents may be added, such as the cross-linked polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
- Dragee cores are provided with suitable coatings.
- suitable coatings may be used, which may optionally contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol (PEG), and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
- Dye-stuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
- compositions that can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin, and a plasticizer, such as glycerol or sorbitol.
- the push-fit capsules can contain the active ingredients in admixture with filler 18 41278.601_P17027-02 such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers.
- the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols (PEGs).
- PEGs liquid polyethylene glycols
- stabilizers may be added.
- the terms “a,” “an,” and “the” refer to “one or more” when used in this application, including the claims.
- reference to “a subject” includes a plurality of subjects, unless the context clearly is to the contrary (e.g., a plurality of subjects), and so forth.
- the terms “comprise,” “comprises,” and “comprising” are used in a non-exclusive sense, except where the context requires otherwise.
- the term “include” and its grammatical variants are intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that can be substituted or added to the listed items.
- the term “about,” when referring to a value can be meant to encompass variations of, in some embodiments, ⁇ 100% in some embodiments ⁇ 50%, in some embodiments ⁇ 20%, in some embodiments ⁇ 10%, in some embodiments ⁇ 5%, in some embodiments ⁇ 1%, in some embodiments ⁇ 0.5%, and in some embodiments ⁇ 0.1% from the specified amount, as such variations are appropriate to perform the disclosed methods or employ the disclosed compositions. 19 41278.601_P17027-02 Further, the term “about” when used in connection with one or more numbers or numerical ranges, should be understood to refer to all such numbers, including all numbers in a range and modifies that range by extending the boundaries above and below the numerical values set forth.
- Aclarubicin also known as aclacinomycin A
- AML acute myeloid leukemia
- this action displays selectivity for specific chromatin classes and histone modifications, with aclarubicin selectively inducing histone eviction in 20 41278.601_P17027-02 regions marked by H3-K27 trimethylation at concentrations that do not induce DNA breaks.
- This observation suggested an application of this drug to incurable pediatric brain tumors driven by histone H3 mutations or other cancer types driven by histone H3 K27me3 dysregulation.
- glioblastoma and diffuse midline glioma (also known as diffuse intrinsic pontine glioma, DIPG, when it occurs in the pons) harboring oncogenic histone H3 mutations, particularly the H3-K27M mutation, are tumors with dismal prognosis and no effective treatment options.
- Trials of multiple chemotherapy agents have failed to produce any meaningful improvement in outcome for these tumors, such that DMG remains a uniformly fatal diagnosis with a median survival of less than one year.
- a breakthrough in our understanding of this tumor was the discovery of oncogenic histone H3 mutations encoding replacement of lysine 27 by methionine (K27M).
- the H3- K27M mutant histone is critical to oncogenic transformation in DMG cells, with a dominant effect on the cellular epigenetic program (FIG. 1) leading to loss of gene-repressive chromatin marks, global DNA hypomethylation, and a distinct gene expression profile.
- FOG. 1 cellular epigenetic program
- genetic studies have confirmed that DMG cells are critically dependent on the H3-K27M mutation, such that deletion of H3-K27M completely abolishes the ability of these cells to form tumors.
- Drugs that interfere with H3-K27M mutant histone incorporation into chromatin could revolutionize DMG therapy by directly targeting the root cause of oncogenic transformation.
- aclarubicin is selectively toxic to histone H3-K27M mutant glioma cells at low-nanomolar concentrations (FIG. 2). Further, we have demonstrated that aclarubicin leads to gene expression changes in H3-K27M glioma cells specifically at gene targets dependent on the H3-K27M mutant histone or K27me3-modified chromatin (FIG. 3).
- aclarubicin its brain penetrant formulations, such as albumin-compound aclarubicin or liposomal aclarubicin, or close chemical derivatives, against histone-mutant glioma and other epigenetically-driven cancer types.
- EXAMPLE 2 Synthesis of o-Benzyl Dimethylamino Analog of Daunorubicin The synthesis of an o-benzyl dimethylamino analog of daunorubicin is provided in Scheme 1 immediately herein below: EXAMPLE 3 Summary of Compound 5 Brain/Plasma Pharmacokinetic (PK) Studies Pharmacokinetic studies demonstrated excellent brain penetration of compound 5, in contrast to the known very poor central nervous system penetration of anthracycline drugs.
- PK Pharmacokinetic
- Compound 5 is the O-benzyl N,N-dimethyl analog of daunorubicin shown in Scheme 1.
- a single IV dose (10 mg/kg) was administered to CD1 male mice, in triplicate, and plasma and brain tissue concentrations were assayed at 8 time points (5 min, 15 min, 30 min, 1 hr, 2 hr, 4 hr, 8 hr, and 24 hr post-dose).
- Drug concentration was quantified using LC- MS/MS with an internal standard. Peak plasma concentration was 1320 ⁇ 56 ng/mL and peak brain tissue concentration was 3221 ⁇ 377 ng/g, corresponding to nearly 5 ⁇ M drug concentration in brain tissue.
- the brain tissue concentration was significantly greater than the simultaneously measured plasma concentration through the first hour, with brain/plasma ratios of 2.45 ⁇ 0.35 at 5 min, 1.65 ⁇ 0.35 at 15 min, 1.73 ⁇ 0.64 at 30 min, 1.25 ⁇ 0.29 at 1 hour, 0.97 ⁇ 0.10 at 2 hours, 0.509 ⁇ 0.158 at 4 hours, and 0.709 at 8 hours.
- Plasma T1/2 was 3.24 hours and brain tissue T1/2 was 1.42 hours. Clinical observation of the animals did not identify any abnormality through the entire 24 hour post-dose study period. 22 41278.601_P17027-02 EXAMPLE 4 General Procedures for the Synthesis of Representative Compounds All solvents were reagent grade or HPLC grade.
- Example 6 IC50 Values for Compound 5 and Reference Doxorubicin on the Proliferation of 140 Cancer Cell Lines
- Compound treatment of cells started one day after seeding with a final DMSO concentration of 0.1% and was performed by nanodrop-dispensing using a Tecan Dispenser.
- 0.1% DMSO (solvent) and Staurosporine (1.0E-05M) served as high control (100% viability) and low control (0% viability), respectively.
- Compounds were tested at the following concentrations: 5.00E-06, 1.50E-06, 5.00E-07, 1.50E-07, 5.00E-08, 1.50E-08, 5.00E-09, 1.50E-09 M.
- Cells were cultured in appropriate media, typically DMEM or RPMI-1640 with 10% fetal calf serum.
- appropriate media typically DMEM or RPMI-1640 with 10% fetal calf serum.
- cells were seeded in white cell culture-treated flat and clear bottom 384 well plates and incubated at 37 °C overnight before compounds were added. After incubation for 72 h at 37°C at 5% CO2, cell plates were equilibrated to room temperature for one hour, CellTiterGlo reagent (Promega) was added and luminescence was measured approximately an hour later using a luminometer. Raw data were converted into percent cell viability relative to the high and low control, which were set to 100% and 0%, respectively.
- IC50 calculation was performed using GraphPad Prism software with a variable slope sigmoidal response fitting model using 0% viability as bottom constraint and 100% viability as top constraint. The data are summarized in Table 1 and presented in FIG.13a-FIG.13n.
- Table 1 Determined IC 50 values for compound 5 and reference doxorubicin on the 26 41278.601_P17027-02 Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines 27 41278.601_P17027-02 Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines 28 41278.601_P17027-02 Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines 29 41278.601_P17027-02 Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines REFERENCES All publications, patent applications, patents, and other references mentioned in the specification are indicative of the level of those skilled in the art to which the presently disclosed subject matter pertains.
- EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells, Proceedings of the National Academy of Sciences of the United States of America, 100 (2003), pp. 11606-11611. M. Sasaki, J. Yamaguchi, K. Itatsu, H. Ikeda, Y. Nakanuma, Over-expression of polycomb group protein EZH2 relates to decreased expression of p16 INK4a in cholangiocarcinogenesis in hepatolithiasis, The Journal of Pathology, 215 (2008), pp. 175- 183. S. Varambally, S.M. Dhanasekaran, M. Zhou, T.R. Barrette, C.
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Abstract
N-alkylated anthracycline derivatives and methods of their use for treating a cancer, including a glioblastoma, diffuse midline glioma (DMG), and diffuse intrinsic pontine glioma (DIPG), are disclosed.
Description
ANTI-CANCER ACTION OF N-ALKYLATED ANTHRACYCLINE DERIVATIVES IN CANCERS, INCLUDING GLIOBLASTOMA AND PEDIATRIC DIFFUSE MIDLINE GLIOMA BACKGROUND The anthracycline topoisomerase inhibitor drugs have been cornerstones of anticancer chemotherapy for decades due to their ability to intercalate into DNA, trap topoisomerase enzymes, and induce DNA damage. Doxorubicin, for instance, is prescribed to over 1 million patients worldwide for the treatment of various hematologic and solid tumors. These drugs, however, to date have had limited success in treating brain tumors, such as glioblastomas and diffuse midline glioma. SUMMARY In some aspects, the presently disclosed subject matter provides a compound of formula (I): (I); wherein: X is H
C1-C8 alkyl; R3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof. In particular aspects, the compound of formula (I) is selected from: O
02
O OH O OH . disclosed subject matter provides a pharmaceutical
formulation comprising the compound of formula (I) and a pharmaceutically acceptable carrier. In other aspects, the presently disclosed subject matter provides a method for treating a cancer in a subject in need of treatment thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of formula (I). In some aspects, the cancer is associate with an oncogenic histone H3 mutation. In certain aspects, the cancer is selected from adrenocortical carcinoma, salivary gland cancer, B-lymphoblastic leukemia/lymphoma, leukemia, ampullary cancer, bladder cancer, breast cancer, renal cell carcinoma, cervical cancer, hepatobiliary cancer, cholangiocarcinoma, mature B-cell neoplasms, colorectal cancer, skin cancer, non-melanoma, mature T and NK neoplasms, melanoma, esophagogastric cancer, bone cancer, glioblastoma, head and neck cancer, renal non-clear cell carcinoma, renal clear cell carcinoma, glioma, non-small cell lung cancer, embryonal tumor, pleural mesothelioma, prostate cancer, gastrointestinal neuroendocrine tumor, cancer of unknown primary, pancreatic cancer, endometrial cancer, thymic tumor, soft tissue sarcoma, small cell lung cancer, penile cancer, gastrointestinal stromal tumor, ovarian cancer, uterine sarcoma, small bowel cancer, appendiceal cancer, thyroid cancer, peripheral nervous system, non-Hodgkin lymphoma, ovarian epithelial tumor, miscellaneous neuroepithelial tumor, pheochromocytoma, sarcoma, seminoma, non- seminomatous germ cell tumor, thymic epithelial tumor, ocular melanoma, and Wilms tumor. In some aspects, the cancer is associated with an oncogenic histone H3 lysine 27 to methionine (K27M) mutation. In certain aspects, the cancer is selected from diffuse intrinsic pontine glioma, diffuse midline glioma, and glioblastoma. 2 41278.601_P17027-02
In some aspects, the cancer is associated with an alteration in H3K27me regulators. In certain aspects, the cancer is associated with an overexpression of EZH2. In particular aspects, the cancer is selected from chronic lymphocytic leukemia, myelodysplastic syndrome, acute myeloid leukemia, natural killer/T-cell lymphoma, melanoma, endometrial, prostate, and breast cancer, and neuroblastoma. In some aspects, the cancer is associated with an Ezh2 mutation (H3K27me3 methyltransferase). In certain aspects, the cancer is selected from non-Hodgkin’s lymphoma, T-cell acute lymphoblastic leukemia, myeloproliferative disorders, myeloid leukemia, melanoma, head and neck squamous cell carcinoma, and malignant peripheral nerve sheath tumors. In some aspects, the cancer is associated with a mutation in Polycomb group- associated proteins (H3K27me3 methyltransferase complex). In certain aspects, the cancer is selected from a myeloid leukemia, glioblastoma, non-Hodgkin’s lymphoma, bladder cancer, pancreatic cancer, and multiple myeloma. In some aspects, the cancer is associated with oncogenic deregulation of histone H3 K27me3 modification and Ezh2 activity. In certain aspects, the cancer is small cell lung cancer or non-small cell lung cancer. In particular aspects, the subject is a pediatric patient. Certain aspects of the presently disclosed subject matter having been stated hereinabove, which are addressed in whole or in part by the presently disclosed subject matter, other aspects will become evident as the description proceeds when taken in connection with the accompanying Examples and Drawings as best described herein below. BRIEF DESCRIPTION OF THE FIGURES The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. Having thus described the presently disclosed subject matter in general terms, reference will now be made to the accompanying Figures, which are not necessarily drawn to scale, and wherein: 3 41278.601_P17027-02
FIG. 1A and FIG. 1B show: (FIG. 1A) In H3-K27M mutant diffuse midline glioma (DMG), incorporation of onco-histones into chromatin leads to altered epigenetic regulation and gene expression changes; (FIG. 1B) Without wishing to be bound to any one particular theory, it is thought that aclarubicin can specifically evict H3-K27M mutant histones from chromatin as a novel therapeutic strategy for DMG; FIG. 2 shows dose-response curves of aclarubicin on patient-derived DIPG cell lines (IC50 = 30 nM); FIG. 3A and FIG. 3B show the differential expression of H3-K27M dependent genes following aclarubicin treatment in JHH-DIPG-1 cells. FIG. 3A is a volcano plot: aclarubicin vs. DMSO treatment. FIG. 3B shows differential expression of K27M-dependent genes following Aclarubicin treatment; FIG. 4 shows gene set enrichment in down-regulated genes; FIG. 5 shows MYC expression with HSJD-DIPG-007 cells; FIG. 6 shows pseudo-bulk sc-ATAC-seq analysis; FIG. 7 is an RNA-seq:PCA plot with SF7761 cells; FIG. 8 is HSJD DIPG 007:NND vs. Dauno. Top GSEA enrichment among upregulated genes. In this example, enrichments of gene sets related to oligodenderocyte differentiation; PRC2/EXH2; and DNA damage and anthracycline-induced apoptosis; FIG. 9 is HSJD DIPG 007. Top GSEA enrichment among most down-regulated genes; FIG. 10 is dose-response viability assays of patient-derived diffuse midline glioma cell lines treated with compound 5; FIG. 11 shows the simultaneous downregulation of oncogenic drivers of diffuse midline glioma by compound 5. Patient-derived DMG neurosphere cell line HSJD-DIPG- 007 was treated with DMSO control or indicated concentrations of compound 5 for 24 hours. Western blotting for indicated protein targets was performed. GAPDH is used as a protein loading control. We observe downregulation of known oncogenic drivers of DMG including PDGFR-β, c-Myc, Olig2, EGFR, along with upregulation of the cyclin-dependent kinase inhibitor p21; FIG. 12 shows reduction in DNA damage (double-strand DNA breaks) induced by compound 5 and aclarubicin as compared to daunorubicin; Cell line JHH-DIPG-1 was 4 41278.601_P17027-02
treated with DMSO control, aclarubicin (Acla), daunorubicin (Dauno), or compound 5 at the 250 nM, 500 nM, or 1 µM, as indicated, for 24 hours, and Western blotting for indicated protein targets was performed. GAPDH is used as a protein loading control. Phospho- H2AX is a marker of the double-strand DNA break response. We observe induction of DNA damage with markedly increased phospho-H2AX with daunorubicin treatment, and a dramatic reduction in DNA damage upon aclarubicin or compound 5 treatment; and FIG. 13a, FIG. 13b, FIG. 13c, FIG. 13d, FIG. 13e, FIG. 13f, FIG. 13g, FIG. 13h, FIG. 13i, FIG. 13j, FIG. 13k, FIG. 13l, FIG. 13m, and FIG. 13n show IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines. DETAILED DESCRIPTION The presently disclosed subject matter now will be described more fully hereinafter with reference to the accompanying Figures, in which some, but not all embodiments of the inventions are shown. Like numbers refer to like elements throughout. The presently disclosed subject matter may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Indeed, many modifications and other embodiments of the presently disclosed subject matter set forth herein will come to mind to one skilled in the art to which the presently disclosed subject matter pertains having the benefit of the teachings presented in the foregoing descriptions and the associated Figures. Therefore, it is to be understood that the presently disclosed subject matter is not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. A. N-alkylated anthracycline derivatives of Formula (I) In some embodiments, the presently disclosed subject matter provides a compound of formula (I): 5 41278.601_P17027-02
I); wherein: X is H y C1-C8 alkyl; R3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof. As used herein, C1-C8 alkyl includes methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, sec-pentyl, isopentyl, neopentyl, n-hexyl, sec-hexyl, n-heptyl, and n-octyl. In particular embodiments, the compound of formula (I) is selected from: O OH O
blood-brain barrier penetration and exhibit specific gene expression effect (downregulates aberrantly expressed onco-histone targets, induces differentiation, and the like). B. Methods for Treating Cancer In some embodiments, the presently disclosed subject matter provides a method for treating a cancer in a subject in need of treatment thereof, the method comprising 6 41278.601_P17027-02
administering to the subject a therapeutically effective amount of a compound of formula (I):. ; wherein: X is H or C1-C8 alkyl; R3 is benzyl;
and stereoisomers and pharmaceutically effective salts thereof. In particular embodiments, the compound of formula (I) is selected from: O OH O
The presently disclosed compounds, in some embodiments, can be used to treat primary brain cancers, brain metastases of other solid tumors, and hematologic malignancies. Alterations of histone H3 K27 methylation are observed in a wide range of cancers, which may be targeted by these compounds. The general relevance of histone H3 K27me alterations across a wide variety of cancer types has been the subjected of multiple in-depth scientific reviews. See Nichol et al., 2016; Shen and Laird, 2013. 7 41278.601_P17027-02
More particularly, the presently disclosed compounds can be used to treat cancers with oncogenic Histone H3 mutations including, but not limited to histone mutations in human tumors selected from adrenocortical carcinoma, salivary gland cancer, B- lymphoblastic leukemia/lymphoma, leukemia, ampullary cancer, bladder cancer, breast cancer, renal cell carcinoma, cervical cancer, hepatobiliary cancer, cholangiocarcinoma, mature B-cell neoplasms, colorectal cancer, skin cancer, non-melanoma, mature T and NK neoplasms, melanoma, esophagogastric cancer, bone cancer, glioblastoma, head and neck cancer, renal non-clear cell carcinoma, renal clear cell carcinoma, glioma, non-small cell lung cancer, embryonal tumor, pleural mesothelioma, prostate cancer, gastrointestinal neuroendocrine tumor, cancer of unknown primary, pancreatic cancer, endometrial cancer, thymic tumor, soft tissue sarcoma, small cell lung cancer, penile cancer, gastrointestinal stromal tumor, ovarian cancer, uterine sarcoma, small bowel cancer, appendiceal cancer, thyroid cancer, peripheral nervous system, non-Hodgkin lymphoma, ovarian epithelial tumor, miscellaneous neuroepithelial tumor, pheochromocytoma, sarcoma, seminoma, non- seminomatous germ cell tumor, thymic epithelial tumor, ocular melanoma, and Wilms tumor. In particular embodiments, the cancer is related to an oncogenic histone H3 lysine 27 to methionine (K27M) mutation in diffuse intrinsic pontine glioma, diffuse midline glioma, and glioblastoma. In other embodiments, the presently disclosed compounds can be used to treat cancers with alterations in H3K27me regulators, including overexpression of EZH2 in chronic lymphocytic leukemia, myelodysplastic syndrome, acute myeloid leukemia, natural killer/T-cell lymphoma, melanoma, endometrial, prostate, and breast cancer, and neuroblastoma. See Bachmann et al., 2006; Kleer et al., 2003; Sasaki et al., 2008; Varambally et al., 2002; Wang et al., 2012; Zingg et al., 2015. In other embodiments, the presently disclosed compounds can be used to treat cancers with Ezh2 mutations (H3K27me3 methyltransferase) including, but not limited to, non-Hodgkin’s lymphoma, T-cell acute lymphoblastic leukemia, myeloproliferative disorders, myeloid leukemia, melanoma, head and neck squamous cell carcinoma, and malignant peripheral nerve sheath tumors. See Morin et al., 2010; Sneeringer et al., 2010; Ernst et al., 2010; Nikoloski et al., 2010; Hodis et al., 2012. 8 41278.601_P17027-02
In other embodiments, the presently disclosed compounds can be used to treat cancers with mutations in Polycomb group-associated proteins (H3K27me3 methyltransferase complex) including, but not limited to, myeloid leukemias, glioblastoma, non-Hodgkin’s lymphoma, bladder cancer, pancreatic cancer, and multiple myeloma. See Waddell et al., 2015; and Guo et al., 2013; van Haaften et al., 2009. In other embodiments, the presently disclosed compounds can be used to treat cancers with oncogenic deregulation of histone H3 K27me3 modification and Ezh2 activity including, but not limited to, small cell lung cancer and non-small cell lung cancer. See Zhang et al., 2016. In particular embodiments, the subject is a pediatric patient. As used herein, the term “treating” can include reversing, alleviating, inhibiting the progression of, preventing or reducing the likelihood of the disease, disorder, or condition to which such term applies, or one or more symptoms or manifestations of such disease, disorder or condition. Preventing refers to causing a disease, disorder, condition, or symptom or manifestation of such, or worsening of the severity of such, not to occur. Accordingly, the presently disclosed compounds can be administered prophylactically to prevent or reduce the incidence or recurrence of the disease, disorder, or condition. In general, the “therapeutically effective amount” of an active agent or drug delivery device refers to the amount necessary to elicit the desired biological response. As will be appreciated by those of ordinary skill in this art, the effective amount of an agent or device may vary depending on such factors as the desired biological endpoint, the agent to be delivered, the makeup of the pharmaceutical composition, the target tissue, and the like. The “subject” treated by the presently disclosed methods in their many embodiments is desirably a human subject, although it is to be understood that the methods described herein are effective with respect to all vertebrate species, which are intended to be included in the term “subject.” Accordingly, a “subject” can include a human subject for medical purposes, such as for the treatment of an existing condition or disease or the prophylactic treatment for preventing the onset of a condition or disease, or an animal subject for medical, veterinary purposes, or developmental purposes. Suitable animal subjects include mammals including, but not limited to, primates, e.g., humans, monkeys, apes, and the like; bovines, e.g., cattle, oxen, and the like; ovines, e.g., sheep and the like; caprines, e.g., goats 9 41278.601_P17027-02
and the like; porcines, e.g., pigs, hogs, and the like; equines, e.g., horses, donkeys, zebras, and the like; poultry, such as domestic fowls including, but not limited to chickens, turkeys, geese, ducks, quail, guinea fowl, and pigeons; felines, including wild and domestic cats; canines, including dogs; lagomorphs, including rabbits, hares, and the like; and rodents, including mice, rats, and the like. An animal may be a transgenic animal. In some embodiments, the subject is a human including, but not limited to, fetal, neonatal, infant, juvenile, and adult subjects. Further, a “subject” can include a patient afflicted with or suspected of being afflicted with a condition or disease. Thus, the terms “subject” and “patient” are used interchangeably herein. The term “subject” also refers to an organism, tissue, cell, or collection of cells from a subject. In particular embodiments, the subject is a human subject. In certain embodiments, the subject is an adult subject. In certain embodiments, the subject is an infant or pediatric subject. In certain embodiments, the subject has an age selected from about 16 years of age or less, about 12 years of age or less, about 8 years of age or less, about 5 years of age or less, and about 2 years of age or less. In some embodiments, the subject is a pediatric patient. As used herein, the term “pediatric” refers to a patient aged 21 or younger at the time of their diagnosis or treatment. Pediatric subpopulations are further categorized as follows: neonates - from birth through the first 28 days of life; infants - 29 days to less than 2 years; children - 2 years to less than 12 years; and adolescents - aged 12 through 21 (up to but not including the 22nd birthday). The term “combination” is used in its broadest sense and means that a subject is administered at least two agents, more particularly a compound described herein and at least one other therapeutic agent. More particularly, the term “in combination” refers to the concomitant administration of two (or more) active agents for the treatment of a, e.g., single disease state. As used herein, the active agents may be combined and administered in a single dosage form, may be administered as separate dosage forms at the same time, or may be administered as separate dosage forms that are administered alternately or sequentially on the same or separate days. In one embodiment of the presently disclosed subject matter, the active agents are combined and administered in a single dosage form. In another embodiment, the active agents are administered in separate dosage forms (e.g., wherein it is 10 41278.601_P17027-02
desirable to vary the amount of one but not the other). The single dosage form may include additional active agents for the treatment of the disease state. Further, the compositions described herein can be administered alone or in combination with adjuvants that enhance stability of the compositions, alone or in combination with one or more therapeutic agents, facilitate administration of pharmaceutical compositions containing them in certain embodiments, provide increased dissolution or dispersion, increase inhibitory activity, provide adjunct therapy, and the like, including other active ingredients. Advantageously, such combination therapies utilize lower dosages of the conventional therapeutics, thus avoiding possible toxicity and adverse side effects incurred when those agents are used as monotherapies. The timing of administration of a compound described herein and at least one additional therapeutic agent can be varied so long as the beneficial effects of the combination of these agents are achieved. Accordingly, the phrase “in combination with” refers to the administration of a compound described herein and at least one additional therapeutic agent either simultaneously, sequentially, or a combination thereof. Therefore, a subject administered a combination of a compound described herein and at least one additional therapeutic agent can receive a compound and at least one additional therapeutic agent at the same time (i.e., simultaneously) or at different times (i.e., sequentially, in either order, on the same day or on different days), so long as the effect of the combination of both agents is achieved in the subject. When administered sequentially, the agents can be administered within 1, 5, 10, 30, 60, 120, 180, 240 minutes or longer of one another. In other embodiments, agents administered sequentially, can be administered within 1, 5, 10, 15, 20 or more days of one another. Where the compound described herein and at least one additional therapeutic agent are administered simultaneously, they can be administered to the subject as separate pharmaceutical compositions, each comprising either a compound or at least one additional therapeutic agent, or they can be administered to a subject as a single pharmaceutical composition comprising both agents. When administered in combination, the effective concentration of each of the agents to elicit a particular biological response may be less than the effective concentration of each agent when administered alone, thereby allowing a reduction in the dose of one or more of 11 41278.601_P17027-02
the agents relative to the dose that would be needed if the agent was administered as a single agent. The effects of multiple agents may, but need not be, additive or synergistic. The agents may be administered multiple times. In some embodiments, when administered in combination, the two or more agents can have a synergistic effect. As used herein, the terms “synergy,” “synergistic,” “synergistically” and derivations thereof, such as in a “synergistic effect” or a “synergistic combination” or a “synergistic composition” refer to circumstances under which the biological activity of a combination of a compound described herein and at least one additional therapeutic agent is greater than the sum of the biological activities of the respective agents when administered individually. Synergy can be expressed in terms of a “Synergy Index (SI),” which generally can be determined by the method described by F. C. Kull et al., Applied Microbiology 9, 538 (1961), from the ratio determined by: Qa/QA + Qb/QB = Synergy Index (SI) wherein: QA is the concentration of a component A, acting alone, which produced an end point in relation to component A; Qa is the concentration of component A, in a mixture, which produced an end point; QB is the concentration of a component B, acting alone, which produced an end point in relation to component B; and Qb is the concentration of component B, in a mixture, which produced an end point. Generally, when the sum of Qa/QA and Qb/QB is greater than one, antagonism is indicated. When the sum is equal to one, additivity is indicated. When the sum is less than one, synergism is demonstrated. The lower the SI, the greater the synergy shown by that particular mixture. Thus, a “synergistic combination” has an activity higher that what can be expected based on the observed activities of the individual components when used alone. Further, a “synergistically effective amount” of a component refers to the amount of the component necessary to elicit a synergistic effect in, for example, another therapeutic agent present in the composition. C. Pharmaceutical formulations and method of administration. 12 41278.601_P17027-02
In other embodiments, the presently disclosed subject matter provides a pharmaceutical formulation comprising the compound of formula (I) and a pharmaceutically acceptable carrier. One of skill in the art will recognize that the pharmaceutical compositions include the pharmaceutically acceptable salts of the compounds described above. Pharmaceutically acceptable salts are generally well known to those of ordinary skill in the art, and include salts of active compounds which are prepared with relatively nontoxic acids or bases, depending on the particular substituent moieties found on the compounds described herein. When compounds of the present disclosure contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent or by ion exchange, whereby one basic counterion (base) in an ionic complex is substituted for another. Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. When compounds of the present disclosure contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent or by ion exchange, whereby one acidic counterion (acid) in an ionic complex is substituted for another. Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p- toluenesulfonic, citric, tartaric, methanesulfonic, trifluoroacetic acid (TFA), and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al, “Pharmaceutical Salts”, Journal of Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds of the present disclosure contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts. Accordingly, pharmaceutically acceptable salts suitable for use with the presently 13 41278.601_P17027-02
disclosed subject matter include, by way of example but not limitation, acetate, benzenesulfonate, benzoate, bicarbonate, bitartrate, bromide, calcium edetate, camsylate, carbonate, citrate, edetate, edisylate, estolate, esylate, fumarate, gluceptate, gluconate, glutamate, glycollylarsanilate, hexylresorcinate, hydrabamine, hydrobromide, hydrochloride, hydroxynaphthoate, iodide, isethionate, lactate, lactobionate, malate, maleate, mandelate, mesylate, mucate, napsylate, nitrate, pamoate (embonate), pantothenate, phosphate/diphosphate, polygalacturonate, salicylate, stearate, subacetate, succinate, sulfate, tannate, tartrate, or teoclate. Other pharmaceutically acceptable salts may be found in, for example, Remington: The Science and Practice of Pharmacy (20th ed.) Lippincott, Williams & Wilkins (2000). In therapeutic and/or diagnostic applications, the compounds of the disclosure can be formulated for a variety of modes of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remington: The Science and Practice of Pharmacy (20th ed.) Lippincott, Williams & Wilkins (2000). Depending on the specific conditions being treated, such agents may be formulated into liquid or solid dosage forms and administered systemically or locally. The agents may be delivered, for example, in a timed- or sustained-slow release form as is known to those skilled in the art. Techniques for formulation and administration may be found in Remington: The Science and Practice of Pharmacy (20th ed.) Lippincott, Williams & Wilkins (2000). Suitable routes may include oral, buccal, by inhalation spray, sublingual, rectal, transdermal, vaginal, transmucosal, nasal or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intra-articullar, intra -sternal, intra-synovial, intra-hepatic, intralesional, intracranial, intraperitoneal, intranasal, or intraocular injections or other modes of delivery. For injection, the agents of the disclosure may be formulated and diluted in aqueous solutions, such as in physiologically compatible buffers such as Hank’s solution, Ringer’s solution, or physiological saline buffer. For such transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. Use of pharmaceutically acceptable inert carriers to formulate the compounds herein 14 41278.601_P17027-02
disclosed for the practice of the disclosure into dosages suitable for systemic administration is within the scope of the disclosure. With proper choice of carrier and suitable manufacturing practice, the compositions of the present disclosure, in particular, those formulated as solutions, may be administered parenterally, such as by intravenous injection. The compounds can be formulated readily using pharmaceutically acceptable carriers well known in the art into dosages suitable for oral administration. Such carriers enable the compounds of the disclosure to be formulated as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject (e.g., patient) to be treated. For nasal or inhalation delivery, the agents of the disclosure also may be formulated by methods known to those of skill in the art, and may include, for example, but not limited to, examples of solubilizing, diluting, or dispersing substances, such as saline; preservatives, such as benzyl alcohol; absorption promoters; and fluorocarbons. In particular embodiments, the presently disclosed compounds are administered intranasally in a form selected from the group consisting of a nasal spray, a nasal drop, a powder, a granule, a cachet, a tablet, an aerosol, a paste, a cream, a gel, an ointment, a salve, a foam, a paste, a lotion, a cream, an oil suspension, an emulsion, a solution, a patch, and a stick. As used herein, the term administrating via an "intranasal route" refers to administering by way of the nasal structures. It has been found that the presently disclosed compounds are much more effective at penetrating the brain when administered intranasally. Intranasal administration generally allows the active agent to bypass first pass metabolism, thereby enhancing the bioavailability of the active agent. Such delivery can offer several advantages over other modes of drug delivery, including, but not limited to, increasing the onset of action, lowering the required dosage, enhancing the efficacy, and improving the safety profile of the active agent. For example, tablet dosage forms enter the bloodstream through the gastrointestinal tract, which subjects the drug to degradation from stomach acid, bile, digestive enzymes, and other first pass metabolism effects. As a result, tablet formulations often require higher doses and generally have a delayed onset of action. Nasal administration of a drug also can facilitate compliance, especially for pediatric patients, geriatric patients, patients suffering from a neurodegenerative disease, or other patients for which swallowing is difficult, e.g., patients suffering from nausea, such as 15 41278.601_P17027-02
patients undergoing chemotherapy, or patients with a swallowing disorder. Intranasal (“i.n.” or “IN”) delivery of an agent to a subject can facilitate delivery of the agent to the brain and/or peripheral nervous system. Such administration is non-invasive and offers several advantages including avoidance of hepatic first pass clearance, rapid onset of action, frequent self-administration and easy dose adjustments. Small molecules have an added advantage of being absorbed paracellularly through the nasal epithelium after which, these molecules can then directly enter the CNS through the olfactory or the trigeminal nerve associated pathway and can be directly transported to the brain upon intranasal administration. For intranasal delivery, in addition to the active ingredients, pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. The agents of the disclosure may be formulated by methods known to those of skill in the art, and may include, for example, but not limited to, examples of solubilizing, diluting, or dispersing substances, such as saline, preservatives, such as benzyl alcohol, absorption promoters, and fluorocarbons. Optimized formulations for intranasal delivery may include addition of permeability enhancers (mucoadhesives, nanoparticles, and the like) as well as combined use with an intranasal drug delivery device (for example, one that provides controlled particle dispersion with particles aerosolized to target the upper nasal cavity). In particular, polymer-based nanoparticles, including chitosan, maltodextrin, polyethylene glycol (PEG), polylactic acid (PLA), polylactic-co-glycolic acid (PLGA), and PAMAM dendrimer; gels, including poloxamer; and lipid-based formulations, including glycerol monocaprate (Capmul™), mixtures of mono-, di-, and triglycerides and mono- and di- fatty esters of PEG (Labrafil™), palmitate, glycerol monostearate, and phospholipids can be used to administer the presently disclosed compounds intranasally. The presently disclosed compounds also can be administered intranasally via mucoadhesive agents. Mucoadhesion is commonly defined as the adhesion between two materials, at least one of which is a mucosal surface. More particularly, mucoadhesion is the interaction between a mucin surface and a synthetic or natural polymer. Mucoadhesive dosage forms can be designed to enable prolonged retention at the site of application, 16 41278.601_P17027-02
providing a controlled rate of drug release for improved therapeutic outcome. Application of dosage forms to mucosal surfaces may be of benefit to drug molecules not amenable to the oral route, such as those that undergo acid degradation or extensive first-pass metabolism. Mucoadhesive materials suitable for use with nasal administration of the presently disclosed compounds include, but are not limited to, soluble cellulose derivatives, such as hydroxypropyl methylcellulose (HPMC), hydroxypropyl cellulose (HPC), methylcellulose (MC), and carboxymethyl cellulose (CMC), and insoluble cellulose derivatives, such as ethylcellulose and microcrystalline cellulose (MCC), starch (e.g., Amioca®), polyacrylates, such as poly(acrylic acid) (e.g., Carbopol® 974P), functionalized mucoadhesive polymers, such as polycarbophil, hyaluronan, and amberlite resin, and chitosan (2-amino-2-deoxy- (l→4)-β-d-glucopyranan) formulations and derivatives thereof. In some embodiments, the formulation also includes a permeability enhancer. As used herein, the term "permeability enhancer" refers to a substance that facilitates the delivery of a drug across mucosal tissue. The term encompasses chemical enhancers that, when applied to the mucosal tissue, render the tissue more permeable to the drug. Permeability enhancers include, but are not limited to, dimethyl sulfoxide (DMSO), hydrogen peroxide (H2O2), propylene glycol, oleic acid, cetyl alcohol, benzalkonium chloride, sodium lauryl sulphate, isopropyl myristate, Tween 80, dimethyl formamide, dimethyl acetamide, sodium lauroylsarcosinate, sorbitan monolaurate, methylsulfonylmethane, Azone, terpenes, phosphatidylcholine dependent phospholipase C, triacyl glycerol hydrolase, acid phosphatase, phospholipase A2, concentrated saline solutions (e.g., PBS and NaCl), polysorbate 80, polysorbate 20, sodium dodecanoate (C12), sodium caprate (CIO) and/or sodium palmitate (CI 6), tert-butyl cyclohexanol (TBCH), and alpha-terpinol. In some embodiments, the intranasal administration is accomplished via a ViaNase™ device (Kurve Technology, Inc.). Pharmaceutical compositions suitable for use in the present disclosure include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. Generally, the compounds according to the disclosure are effective over a wide dosage 17 41278.601_P17027-02
range. For example, in the treatment of adult humans, dosages from 0.01 to 1000 mg, from 0.5 to 100 mg, from 1 to 50 mg per day, and from 5 to 40 mg per day are examples of dosages that may be used. A non-limiting dosage is 10 to 30 mg per day. The exact dosage will depend upon the route of administration, the form in which the compound is administered, the subject to be treated, the body weight of the subject to be treated, the bioavailability of the compound(s), the adsorption, distribution, metabolism, and excretion (ADME) toxicity of the compound(s), and the preference and experience of the attending physician. In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. The preparations formulated for oral administration may be in the form of tablets, dragees, capsules, or solutions. Pharmaceutical preparations for oral use can be obtained by combining the active compounds with solid excipients, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl- cellulose, sodium carboxymethyl-cellulose (CMC), and/or polyvinylpyrrolidone (PVP: povidone). If desired, disintegrating agents may be added, such as the cross-linked polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol (PEG), and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dye-stuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses. Pharmaceutical preparations that can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin, and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler 18 41278.601_P17027-02
such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols (PEGs). In addition, stabilizers may be added. Following long-standing patent law convention, the terms “a,” “an,” and “the” refer to “one or more” when used in this application, including the claims. Thus, for example, reference to “a subject” includes a plurality of subjects, unless the context clearly is to the contrary (e.g., a plurality of subjects), and so forth. Throughout this specification and the claims, the terms “comprise,” “comprises,” and “comprising” are used in a non-exclusive sense, except where the context requires otherwise. Likewise, the term “include” and its grammatical variants are intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that can be substituted or added to the listed items. For the purposes of this specification and appended claims, unless otherwise indicated, all numbers expressing amounts, sizes, dimensions, proportions, shapes, formulations, parameters, percentages, quantities, characteristics, and other numerical values used in the specification and claims, are to be understood as being modified in all instances by the term “about” even though the term “about” may not expressly appear with the value, amount or range. Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are not and need not be exact, but may be approximate and/or larger or smaller as desired, reflecting tolerances, conversion factors, rounding off, measurement error and the like, and other factors known to those of skill in the art depending on the desired properties sought to be obtained by the presently disclosed subject matter. For example, the term “about,” when referring to a value can be meant to encompass variations of, in some embodiments, ± 100% in some embodiments ± 50%, in some embodiments ± 20%, in some embodiments ± 10%, in some embodiments ± 5%, in some embodiments ±1%, in some embodiments ± 0.5%, and in some embodiments ± 0.1% from the specified amount, as such variations are appropriate to perform the disclosed methods or employ the disclosed compositions. 19 41278.601_P17027-02
Further, the term “about” when used in connection with one or more numbers or numerical ranges, should be understood to refer to all such numbers, including all numbers in a range and modifies that range by extending the boundaries above and below the numerical values set forth. The recitation of numerical ranges by endpoints includes all numbers, e.g., whole integers, including fractions thereof, subsumed within that range (for example, the recitation of 1 to 5 includes 1, 2, 3, 4, and 5, as well as fractions thereof, e.g., 1.5, 2.25, 3.75, 4.1, and the like) and any range within that range. EXAMPLES The following Examples have been included to provide guidance to one of ordinary skill in the art for practicing representative embodiments of the presently disclosed subject matter. In light of the present disclosure and the general level of skill in the art, those of skill can appreciate that the following Examples are intended to be exemplary only and that numerous changes, modifications, and alterations can be employed without departing from the scope of the presently disclosed subject matter. The synthetic descriptions and specific examples that follow are only intended for the purposes of illustration, and are not to be construed as limiting in any manner to make compounds of the disclosure by other methods. EXAMPLE 1 Anti-Cancer Action of Aclarubicin and Related Compounds in Cancers with Oncogenic Histone H3 Mutation and/or Alterations in Histone H3 K27me3, including Glioblastoma and Pediatric Diffuse Midline Glioma The presently disclosed subject matter provides, in part, a novel mechanism of action of anthracycline derivatives. Aclarubicin (also known as aclacinomycin A) is an anthracycline compound not currently in clinical use in the United States or Europe, but has been used in Japan, India, and China in the treatment of acute myeloid leukemia (AML), with favorable efficacy and side effect profiles. The presently disclosed subject matter demonstrates that aclarubicin can intercalate into DNA and ‘evict’ or displace histones from loose chromatin structures and induce nucleosome turnover. Remarkably, this action displays selectivity for specific chromatin classes and histone modifications, with aclarubicin selectively inducing histone eviction in 20 41278.601_P17027-02
regions marked by H3-K27 trimethylation at concentrations that do not induce DNA breaks. This observation suggested an application of this drug to incurable pediatric brain tumors driven by histone H3 mutations or other cancer types driven by histone H3 K27me3 dysregulation. Pediatric glioblastoma and diffuse midline glioma (DMG) (also known as diffuse intrinsic pontine glioma, DIPG, when it occurs in the pons) harboring oncogenic histone H3 mutations, particularly the H3-K27M mutation, are tumors with dismal prognosis and no effective treatment options. Trials of multiple chemotherapy agents have failed to produce any meaningful improvement in outcome for these tumors, such that DMG remains a uniformly fatal diagnosis with a median survival of less than one year. A breakthrough in our understanding of this tumor was the discovery of oncogenic histone H3 mutations encoding replacement of lysine 27 by methionine (K27M). The H3- K27M mutant histone is critical to oncogenic transformation in DMG cells, with a dominant effect on the cellular epigenetic program (FIG. 1) leading to loss of gene-repressive chromatin marks, global DNA hypomethylation, and a distinct gene expression profile. Importantly, genetic studies have confirmed that DMG cells are critically dependent on the H3-K27M mutation, such that deletion of H3-K27M completely abolishes the ability of these cells to form tumors. Drugs that interfere with H3-K27M mutant histone incorporation into chromatin could revolutionize DMG therapy by directly targeting the root cause of oncogenic transformation. We have now found that aclarubicin is selectively toxic to histone H3-K27M mutant glioma cells at low-nanomolar concentrations (FIG. 2). Further, we have demonstrated that aclarubicin leads to gene expression changes in H3-K27M glioma cells specifically at gene targets dependent on the H3-K27M mutant histone or K27me3-modified chromatin (FIG. 3). We propose the development and further clinical investigation of aclarubicin, its brain penetrant formulations, such as albumin-compound aclarubicin or liposomal aclarubicin, or close chemical derivatives, against histone-mutant glioma and other epigenetically-driven cancer types. Accordingly, the presently disclosed subject matter provides a novel treatment for currently incurable pediatric brain tumors (e.g., diffuse midline glioma, glioblastoma) and also is relevant to adult glioblastoma and other cancer types. 21 41278.601_P17027-02
EXAMPLE 2 Synthesis of o-Benzyl Dimethylamino Analog of Daunorubicin The synthesis of an o-benzyl dimethylamino analog of daunorubicin is provided in Scheme 1 immediately herein below:
EXAMPLE 3 Summary of Compound 5 Brain/Plasma Pharmacokinetic (PK) Studies Pharmacokinetic studies demonstrated excellent brain penetration of compound 5, in contrast to the known very poor central nervous system penetration of anthracycline drugs. Compound 5 is the O-benzyl N,N-dimethyl analog of daunorubicin shown in Scheme 1. A single IV dose (10 mg/kg) was administered to CD1 male mice, in triplicate, and plasma and brain tissue concentrations were assayed at 8 time points (5 min, 15 min, 30 min, 1 hr, 2 hr, 4 hr, 8 hr, and 24 hr post-dose). Drug concentration was quantified using LC- MS/MS with an internal standard. Peak plasma concentration was 1320 ± 56 ng/mL and peak brain tissue concentration was 3221 ± 377 ng/g, corresponding to nearly 5 µM drug concentration in brain tissue. The brain tissue concentration was significantly greater than the simultaneously measured plasma concentration through the first hour, with brain/plasma ratios of 2.45 ± 0.35 at 5 min, 1.65 ± 0.35 at 15 min, 1.73 ± 0.64 at 30 min, 1.25 ± 0.29 at 1 hour, 0.97 ± 0.10 at 2 hours, 0.509 ± 0.158 at 4 hours, and 0.709 at 8 hours. Plasma T1/2 was 3.24 hours and brain tissue T1/2 was 1.42 hours. Clinical observation of the animals did not identify any abnormality through the entire 24 hour post-dose study period. 22 41278.601_P17027-02
EXAMPLE 4 General Procedures for the Synthesis of Representative Compounds All solvents were reagent grade or HPLC grade. Unless otherwise noted, all materials were obtained from commercial suppliers and used without further purification. Daunorubicin was purchased from Ontario Chemicals. 1H NMR spectra were recorded at 400 MHz or 500 MHz. Chemical shifts are reported in parts per million relative to TMS. Preparative HPLC purification was performed on an Agilent 1200 series HPLC system equipped with an Agilent G1315D diode array detector using a Phenomenex Luna 5 μm C18(2) column (21.2 mm × 250 mm, 5 μm) at a flowrate of 25 mL/min with a gradient of 20% ACN/80% H2O for 5 min followed by an increase to 70% ACN/30% H2O over 40 min. Analytical HPLC was performed on an Agilent 1260 series HPLC system equipped with an Eclipse Plus C18 column (2.1 mm × 50 mm, 3.5 μm) at a flowrate of 1.25 mL/min with a gradient of 20% ACN/80% H2O for 0.25 min followed by an increase to 85% ACN/15% H2O over 1.75 minutes and continuation of 85% ACN/15% H2O until 4 min (detection at 220 nm). EXAMPLE 5 Synthesis of O-Benzyl Dimethylamino Analog of Daunorubicin The synthesis of an O-benzyl dimethylamino analog of daunorubicin 5 is provided in Scheme 1 immediately herein below:
02
Scheme 1. Synthesis of 5. (a) CF3CO2Et, Et3N, MeOH, rt, 1 hr, 91%; (b) (i) NaH, DMF, 0 °C; (ii) BnBr, DCM, 0 °C, 24 hr, 25%; (c) NaOH, THF-water, 50 °C, 1.5 hr; (d) aq. HCHO, NaCNBH3, THF, RT, 10 min, 12% from compound 3. EXAMPLE 6 Synthesis of O-Benzyl Dimethylamino Analog of Daunorubicin 5 3-N-trifluoroacetyl daunorubicin (2) To a solution of daunorubicin•HCl (4.97 g, 8.81 mmol) in methanol (60 mL) at rt was added triethylamine (2.95 mL, 21.2 mmol), followed by a slow addition of ethyl trifluoroacetate (2.94 mL, 24.7 mmol). The reaction mixture was stirred at rt for 1 h, then the solvent was removed in vacuo. A solution of 1 N HCl was added until the color of the reaction turned from dark blue to bright orange, and the compound was extracted twice with chloroform. The combined organic extract was washed with water, dried over sodium sulfate and concentrated to give a solid residue which was triturated in diethyl ether to afford 4.98 g (91% yield) of compound 2 as a bright orange solid. 1H NMR (400 MHz, CDCl3) δ 13.99 (s, 1H), 13.26 (s, 1H), 8.03 (d, J = 6.6 Hz, 1H),
Hz, 1H), 7.39 (d, J = 8.6 Hz, 1H), 6.71 (d, J = 9.2 Hz, 1H), 5.52 (s, 1H), 5.26 (s, 1H), 4.37 – 4.16 (m, 3H), 4.07 (s, 3H), 3.67 (s, 1H), 3.22 (m, 1H), 2.90 (m, 1H), 2.41 (s, 3H), 2.29 (m, 1H), 2.15 (m, 1H), 1.95 (m, 1H), 1.82 (m, 1H), 1.31 (d, J = 6.6 Hz, 3H). 3’-N-trifluoroacetyl-4’-O-benzyldaunorubicin (3) To a solution of 3-N-trifluoroacetyl daunorubicin (4.98 g, 7.99 mmol) in DMF (50 mL) at 0 °C was added portion wise NaH (60% w/w, 4.76 g, 119 mmol, 14.9 mmol). After 5 min stirring, a solution of benzyl bromide (14.2 mL, 120 mmol) in DCM (150 mL) was slowly added over 1 h via additional funnel. At the end of the addition, another 100 mL of DCM was added as the reaction mixture turned too vacuous, thus difficult to stir. The dark blue mixture was stirred at 0 °C for 24 h and the progress of the reaction was monitored by LCMS until by-products started forming. Then a 1:1 AcOH/water was added to the dark blue reaction until the mixture turned bright orange. Water was added and the layers were separated. The organic DCM layer containing some amount of acetic acid was concentrated in vacuo. The residue was co-evaporated several times with DCM and the crude material was purified 3 times by Biotage silica chromatography using a 10-80% EtOAc/hexanes gradient as eluent to afford 1.4 g (25% yield) as a maroon solid. 1H NMR (400 MHz, 24 41278.601_P17027-02
CDCl3) δ 13.97 (s, 1H), 13.26 (s, 1H), 8.03 (d, J = 3.4 Hz, 1H), 7.78 (t, J = 8.1 Hz, 1H), 7.32-7.39 (m, 6H), 6.18 (d, J = 8.5 Hz, 1H); 5.55 (d, J = 3.2 Hz, 1H),), 5.28 (s, 1H), 4.86 (d, J = 11.6 Hz, 1H) 4.45 (d, J = 11.7 Hz, 1H) 4.37 (s, 1H), 4.20 (m, 2H), 4.07 (s, 3H), 3.61 (s, 1H), 3.27 (d, J = 2.1 Hz, 0H) 2.95 (d, J = 2.0 Hz, 1H) 2.43 (s, 3H), 2.30 (m, 1H), 2.15 (m, 1H), 1.97 (m, 1H), 1.82 (m, 1H), 1.38 (d, J = 6.7 Hz, 3H). (8S,10S)-8-acetyl-10-(((2R,4S,5S,6S)-4-amino-5-(benzyloxy)-6-methyltetrahydro-2H-pyran- 2-yl)oxy)-6,8,11-trihydroxy-1-methoxy-7,8,9,10-tetrahydrotetracene-5,12-dione (4) To a solution of compound 3 (0.36 g, 0.50 mmol) in THF (10 mL) was added 1 N NaOH (10.1 mL) and the mixture was heated at 50 °C under N2 for 1.5 h. The reaction was cooled to 0 °C and a solution of 10% KHSO4 was carefully added to bring pH to 7-8, followed by the addition of water. The product was extracted (x 3) with chloroform. Unwanted precipitate was filtered off. The two layers were then separated and the organic layer was dried over sodium sulfate and concentrated in vacuo to give an orange solid which was carried to the next step without further purification. (8S,10S)-8-acetyl-10-(((2R,4S,5S,6S)-5-(benzyloxy)-4-(dimethylamino)-6-methyltetrahydro- 2H-pyran-2-yl)oxy)-6,8,11-trihydroxy-1-methoxy-7,8,9,10-tetrahydrotetracene-5,12-dione (5) A mixture of previously obtained compound 4 (0.50 mmol) and a 37% aqueous solution of formaldehyde (1.22 mL, 15 mmol) was stirred together in THF (10 mL) for 10 min at rt. Then NaCNBH3 (31.4 mg) was added. The color of the reaction gradually turned from bright orange to dark orange/brown. After an additional 10 min stirring, the reaction was complete as monitored by LCMS. Saturated aqueous NaHCO3 solution was added which changed the color of the reaction to purple, followed by a pH adjustment to 7-8 with the addition of 1 N HCl. The mixture was extracted (× 3) with chloroform and the combined organic extract was dried over sodium sulfate and concentrated to a residue, which was purified by preparative HPLC (method: 20-70%_Longer). Impure fractions were combined and repurified (method: 10-50% acetonitrile/water) to give a total of 38 mg (12% overall yield from 3) of compound 5 as a dark orange solid.1H NMR (500 MHz, CDCl3) δ 1H NMR (500 MHz, CDCl3) δ 14.04 (s, 1H), 13.30 (s, 1H), 8.41 (s, 1H), 8.04 (d, J = 7.7 Hz, 1H), 7.79 (t, J = 8.1 Hz, 1H), 7.41 (m, 3H), 7.35 (m, 2H), 7.29 (m, 1H), 5.66 (d, J = 3.7 Hz, 1H), 5.26 (dd, J = 4.4, 2.0 Hz, 1H), 4.90 – 4.72 (m, 2H), 4.17 – 4.02 (m, 6H), 3.28 – 3.17 (m, 25 41278.601_P17027-02
2H), 2.94 (d, J = 18.7 Hz, 1H), 2.56 (s, 6H), 2.42 (s, 3H), 2.34 – 2.26 (m, 1H), 2.22 (td, J = 12.9, 4.0 Hz, 1H), 2.14 (dd, J = 14.9, 4.4 Hz, 1H), 1.81 (d, J = 3.6 Hz, 1H), 1.30 (d, J = 6.5 Hz, 3H).13C NMR (126 MHz, CDCl3) δ 212.11, 187.34, 186.88, 161.21, 156.68, 156.07, 138.24, 135.88, 135.74, 134.70, 134.41, 128.51, 128.13, 127.87, 121.12, 119.98, 118.52, 111.61, 111.45, 100.87, 76.16, 74.60, 69.82, 69.04, 60.25, 56.84, 41.94, 35.17, 33.47, 26.07, 24.98, 17.63. LC/MS: >99% by area, retention time 1.71 min, m/z 646.3 [M + H]+. Example 6 IC50 Values for Compound 5 and Reference Doxorubicin on the Proliferation of 140 Cancer Cell Lines Compound treatment of cells started one day after seeding with a final DMSO concentration of 0.1% and was performed by nanodrop-dispensing using a Tecan Dispenser. 0.1% DMSO (solvent) and Staurosporine (1.0E-05M) served as high control (100% viability) and low control (0% viability), respectively. Compounds were tested at the following concentrations: 5.00E-06, 1.50E-06, 5.00E-07, 1.50E-07, 5.00E-08, 1.50E-08, 5.00E-09, 1.50E-09 M. Cells were cultured in appropriate media, typically DMEM or RPMI-1640 with 10% fetal calf serum. For the assays, cells were seeded in white cell culture-treated flat and clear bottom 384 well plates and incubated at 37 °C overnight before compounds were added. After incubation for 72 h at 37°C at 5% CO2, cell plates were equilibrated to room temperature for one hour, CellTiterGlo reagent (Promega) was added and luminescence was measured approximately an hour later using a luminometer. Raw data were converted into percent cell viability relative to the high and low control, which were set to 100% and 0%, respectively. IC50 calculation was performed using GraphPad Prism software with a variable slope sigmoidal response fitting model using 0% viability as bottom constraint and 100% viability as top constraint. The data are summarized in Table 1 and presented in FIG.13a-FIG.13n. Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the
26 41278.601_P17027-02
Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines
27 41278.601_P17027-02
Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines
28 41278.601_P17027-02
Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines
29 41278.601_P17027-02
Table 1: Determined IC50 values for compound 5 and reference doxorubicin on the proliferation of 140 cancer cell lines
REFERENCES All publications, patent applications, patents, and other references mentioned in the specification are indicative of the level of those skilled in the art to which the presently disclosed subject matter pertains. All publications, patent applications, patents, and other references are herein incorporated by reference to the same extent as if each individual publication, patent application, patent, and other reference was specifically and individually indicated to be incorporated by reference. It will be understood that, although a number of patent applications, patents, and other references are referred to herein, such reference does not constitute an admission that any of these documents form part of the common general knowledge in the art. Nichol JN, Dupéré-Richer D, Ezponda T, Licht JD, Miller WH Jr. H3K27 Methylation: A Focal Point of Epigenetic Deregulation in Cancer. Adv Cancer Res. 2016;131:59-95. doi: 10.1016/bs.acr.2016.05.001. Epub 2016 Jun 17. PMID: 27451124; PMCID: PMC5325795. Shen H, Laird PW. Interplay between the cancer genome and epigenome. Cell. 2013 Mar 28;153(1):38-55. doi: 10.1016/j.cell.2013.03.008. PMID: 23540689; PMCID: PMC3648790. 30 41278.601_P17027-02
Nacev BA, Feng L, Bagert JD, Lemiesz AE, Gao J, Soshnev AA, Kundra R, Schultz N, Muir TW, Allis CD. The expanding landscape of 'oncohistone' mutations in human cancers. Nature. 2019 Mar;567(7749):473-478. doi: 10.1038/s41586-019-1038-1. Epub 2019 Mar 20. PMID: 30894748; PMCID: PMC6512987. I.M. Bachmann, O.J. Halvorsen, K. Collett, I.M. Stefansson, O. Straume, S.A. Hauka as, et al., EZH2 expression is associated with high proliferation rate and aggressive tumor subgroups in cutaneous melanoma and cancers of the endometrium, prostate, and breast. Journal of Clinical Oncology, 24 (2006), pp. 268-273. C.G. Kleer, Q. Cao, S. Varambally, R. Shen, I. Ota, S.A. Tomlins, et al., EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells, Proceedings of the National Academy of Sciences of the United States of America, 100 (2003), pp. 11606-11611. M. Sasaki, J. Yamaguchi, K. Itatsu, H. Ikeda, Y. Nakanuma, Over-expression of polycomb group protein EZH2 relates to decreased expression of p16 INK4a in cholangiocarcinogenesis in hepatolithiasis, The Journal of Pathology, 215 (2008), pp. 175- 183. S. Varambally, S.M. Dhanasekaran, M. Zhou, T.R. Barrette, C. Kumar- Sinha, M.G. Sanda, et al., The polycomb group protein EZH2 is involved in progression of prostate cancer, Nature, 419 (2002), pp. 624-629. C. Wang, Z. Liu, C.W. Woo, Z. Li, L. Wang, J.S. Wei, et al., EZH2 mediates epigenetic silencing of neuroblastoma suppressor genes CASZ1, CLU, RUNX3, and NGFR, Cancer Research, 72 (2012), pp. 315-324. D. Zingg, J. Debbache, S.M. Schaefer, E. Tuncer, S.C. Frommel, P. Chen, et al., The epigenetic modifier EZH2 controls melanoma growth and metastasis through silencing of distinct tumour suppressors, Nature Communications, 6 (2015), p. 6051. R.D. Morin, N.A. Johnson, T.M. Severson, A.J. Mungall, J. An, R. Goya, et al., Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin, Nature Genetics, 42 (2010), pp. 181-185 C.J. Sneeringer, M.P. Scott, K.W. Kuntz, S.K. Knutson, R.M. Pollock, V.M. Richon, et al., Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas, 31 41278.601_P17027-02
Proceedings of the National Academy of Sciences of the United States of America, 107 (2010), pp. 20980-20985. T. Ernst, A.J. Chase, J. Score, C.E. Hidalgo-Curtis, C. Bryant, A.V. Jones, et al., Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders, Nature Genetics, 42 (2010), pp. 722-726. G. Nikoloski, S.M. Langemeijer, R.P. Kuiper, R. Knops, M. Massop, E.R. Tonnissen, et al., Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes, Nature Genetics, 42 (2010), pp. 665-667. P. Ntziachristos, A. Tsirigos, P. Van Vlierberghe, J. Nedjic, T. Trimarchi, M.S. Flaherty, et al., Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia, Nature Medicine, 18 (2012), pp. 298-301. E. Hodis, I.R. Watson, G.V. Kryukov, S.T. Arold, M. Imielinski, J.P. Theurillat, et al., A landscape of driver mutations in melanoma, Cell, 150 (2012), pp. 251-263. N. Waddell, M. Pajic, A.M. Patch, D.K. Chang, K.S. Kassahn, P. Bailey, et al., Whole genomes redefine the mutational landscape of pancreatic cancer, Nature, 518 (2015), pp. 495-501. G. Guo, X. Sun, C. Chen, S. Wu, P. Huang, Z. Li, et al., Whole-genome and whole- exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation, Nature Genetics, 45 (2013), pp. 1459-1463. G. van Haaften, G.L. Dalgliesh, H. Davies, L. Chen, G. Bignell, C. Greenman, et al., Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer, Nature Genetics, 41 (2009), pp. 521-523. Zhang H, Qi J, Reyes JM, Li L, Rao PK, Li F, Lin CY, Perry JA, Lawlor MA, Federation A, De Raedt T, Li YY, Liu Y, Duarte MA, Zhang Y, Herter-Sprie GS, Kikuchi E, Carretero J, Perou CM, Reibel JB, Paulk J, Bronson RT, Watanabe H, Brainson CF, Kim CF, Hammerman PS, Brown M, Cichowski K, Long H, Bradner JE, Wong KK. Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer. Cancer Discov. 2016 Sep;6(9):1006-21. doi: 10.1158/2159-8290.CD-16-0164. Epub 2016 Jun 16. PMID: 27312177; PMCID: PMC5010480. International PCT Published Patent Application No. WO2008/029294 for Method of Producing Anthracycline Derivatives to Szeja, published March 13, 2008. 32 41278.601_P17027-02
Although the foregoing subject matter has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be understood by those skilled in the art that certain changes and modifications can be practiced within the scope of the appended claims. 33 41278.601_P17027-02
Claims
THAT WHICH IS CLAIMED: 1. A compound of formula (I): (I); wherein:
X is H or OH; R1 and R2 are each independently C1-C8 alkyl; R3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof.
2. The compound of claim 1, wherein the compound of formula (I) is selected from: O OH O
3. A pharmaceutical formulation comprising the compound of claim 1 or claim 2 and a pharmaceutically acceptable carrier.
34 41278.601_P17027-02
4. A method for treating a cancer in a subject in need of treatment thereof, the method comprising administering to the subject a therapeutically effective amount of a compound of formula (I): ; wherein:
X is H or OH; R1 and R2 are each independently C1-C8 alkyl; R3 is benzyl; and stereoisomers and pharmaceutically effective salts thereof.
5. The method of claim 4, wherein the compound of formula (I) is selected from: O OH O
02
6. The method of claim 4, wherein the cancer is associate with an oncogenic histone H3 mutation.
7. The method of claim 6, wherein the cancer is selected from adrenocortical carcinoma, salivary gland cancer, B-lymphoblastic leukemia/lymphoma, leukemia, ampullary cancer, bladder cancer, breast cancer, renal cell carcinoma, cervical cancer, hepatobiliary cancer, cholangiocarcinoma, mature B-cell neoplasms, colorectal cancer, skin cancer, non-melanoma, mature T and NK neoplasms, melanoma, esophagogastric cancer, bone cancer, glioblastoma, head and neck cancer, renal non-clear cell carcinoma, renal clear cell carcinoma, glioma, non-small cell lung cancer, embryonal tumor, pleural mesothelioma, prostate cancer, gastrointestinal neuroendocrine tumor, cancer of unknown primary, pancreatic cancer, endometrial cancer, thymic tumor, soft tissue sarcoma, small cell lung cancer, penile cancer, gastrointestinal stromal tumor, ovarian cancer, uterine sarcoma, small bowel cancer, appendiceal cancer, thyroid cancer, peripheral nervous system, non-Hodgkin lymphoma, ovarian epithelial tumor, miscellaneous neuroepithelial tumor, pheochromocytoma, sarcoma, seminoma, non-seminomatous germ cell tumor, thymic epithelial tumor, ocular melanoma, and Wilms tumor.
8. The method of claim 4, wherein the cancer is associated with an oncogenic histone H3 lysine 27 to methionine (K27M) mutation.
9. The method of claim 8, wherein the cancer is selected from diffuse intrinsic pontine glioma, diffuse midline glioma, and glioblastoma.
10. The method of claim 4, wherein the cancer is associated with an alteration in H3K27me regulators.
11. The method of claim 10, wherein the cancer is associated with an overexpression of EZH2.
36 41278.601_P17027-02
12. The method of claim 11, wherein the cancer is selected from chronic lymphocytic leukemia, myelodysplastic syndrome, acute myeloid leukemia, natural killer/T- cell lymphoma, melanoma, endometrial, prostate, and breast cancer, and neuroblastoma.
13. The method of claim 4, wherein the cancer is associated with an Ezh2 mutation (H3K27me3 methyltransferase).
14. The method of claim 13, wherein the cancer is selected from non-Hodgkin’s lymphoma, T-cell acute lymphoblastic leukemia, myeloproliferative disorders, myeloid leukemia, melanoma, head and neck squamous cell carcinoma, and malignant peripheral nerve sheath tumors.
15. The method of claim 4, wherein the cancer is associated with a mutation in Polycomb group-associated proteins (H3K27me3 methyltransferase complex).
16. The method of claim 15, wherein the cancer is selected from a myeloid leukemia, glioblastoma, non-Hodgkin’s lymphoma, bladder cancer, pancreatic cancer, and multiple myeloma.
17. The method of claim 4, wherein the cancer is associated with oncogenic deregulation of histone H3 K27me3 modification and Ezh2 activity.
18. The method of claim 17, wherein the cancer is small cell lung cancer or non- small cell lung cancer.
19. The method of any one of claims 4 to 18, wherein the subject is a pediatric patient.
37 41278.601_P17027-02
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