WO2021007286A1 - Compositions and methods for cancer therapy - Google Patents

Compositions and methods for cancer therapy Download PDF

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Publication number
WO2021007286A1
WO2021007286A1 PCT/US2020/041139 US2020041139W WO2021007286A1 WO 2021007286 A1 WO2021007286 A1 WO 2021007286A1 US 2020041139 W US2020041139 W US 2020041139W WO 2021007286 A1 WO2021007286 A1 WO 2021007286A1
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cancer
compound
tyrosine kinase
daltons
arg
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PCT/US2020/041139
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French (fr)
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Hai RAO
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Board Of Regents, The University Of Texas System
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    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/542Carboxylic acids, e.g. a fatty acid or an amino acid
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/545Heterocyclic compounds
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/55Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug, i.e. a dimer, oligomer or polymer of pharmacologically or therapeutically active compounds
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D239/00Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
    • C07D239/70Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings condensed with carbocyclic rings or ring systems
    • C07D239/72Quinazolines; Hydrogenated quinazolines
    • C07D239/86Quinazolines; Hydrogenated quinazolines with hetero atoms directly attached in position 4
    • C07D239/94Nitrogen atoms
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D277/00Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings
    • C07D277/02Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings
    • C07D277/20Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
    • C07D277/32Heterocyclic compounds containing 1,3-thiazole or hydrogenated 1,3-thiazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D277/34Oxygen atoms
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D403/00Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/12Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D417/00Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/02Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
    • C07D417/12Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D417/00Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
    • C07D417/14Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing three or more hetero rings

Definitions

  • the present disclosure relates to compositions and methods for treating cancers.
  • ubiquitin ligase (E3) recognizes its target and covalently attaches ubiquitin, a conserved 76-residue protein, onto the substrate, leading to subsequent degradation by the proteasome, a multi-subunit protease.
  • E3 ubiquitin ligase
  • the small molecule is composed of a ligand for the target protein and a moiety that binds a ubiquitin ligase, which can trigger target destruction.
  • an adapter molecule was designed to bring ERRa to a ubiquitin ligase E3 (i.e., VHL) for destruction in mammalian cells and mouse xenograft models (Figs. IB ID). The study overcame a major roadblock in the therapeutic potential of protein knockdown approach.
  • the PROTAC adds a degradation signal that rapidly destroys the target, thereby limiting the time of drug engagement and reducing the risk that acquired defects accumulate and phenotypes are reversed ii) difficulty in monitoring and/or blocking target activity.
  • Many cancer targets don’t have obvious enzymatic activity (e.g., kinase) that could be easily assayed in vivo and in vitro, making it hard to monitor the effects of inhibitors.
  • the PROTAC requires neither the direct inhibition of target activity nor the stable drug-target interaction since the target would be destroyed on contact upon drug exposure. Therefore, the PROTAC can be used on any molecule that can recognize relevant disease targets via the appendage of additional degradation moiety.
  • the disclosed subject matter in one aspect, relates to compounds, compositions and methods of making and using compounds and compositions.
  • X is a destabilization amino acid residue
  • Y is a linker
  • Z is a ligand that binds a tyrosine kinase
  • the destabilization amino acid residue is selected from the group consisting of Arg, His, Lys, Leu, lie, Phe, Trp, Tyr, Cys, Asn, Asp, Glu, and Gin.
  • the destabilization amino acid residue is Arg or His.
  • the tyrosine kinase is a receptor tyrosine kinase or a non-receptor tyrosine kinase.
  • the receptor tyrosine kinase comprises estrogen-related receptor a or epidermal growth factor receptor.
  • the ligand comprises an anti-cancer drug.
  • the anti-cancer drug comprises gefitinib, dasatinib, imatinib, crizotinib, lapatinib, or a thiazolidinedione derivative.
  • the compound has a molecular weight no more than 1000 daltons.
  • the compound is selected from the group consisting of
  • composition comprising: the compound of any preceding aspect; and a pharmaceutically acceptable carrier.
  • a method for treating a cancer in a subject in need thereof comprising: administering a therapeutically effective amount of the pharmaceutical composition of any preceding aspect.
  • the cancer comprises chronic myeloid leukemia, acute lymphocytic leukemia, breast cancer, or lung cancer.
  • the subject is a human.
  • a method of treating a cancer in a subject in need thereof comprising: administering a therapeutically effective amount of a compound of Formula I:
  • X is a destabilization amino acid residue
  • Y is a linker
  • Z is a ligand that binds a tyrosine kinase
  • Figs. 1A-1D show targeting estrogen-related receptor a (ERRa) for destruction.
  • Fig. 1A shows that in ubiquitin (Ub)-mediated degradation, a Ub ligase E3 binds the substrate and put on a chain of Ub molecules (red dots), a molecular marker for the proteasome, with the help of El and E2 enzymes. Ub-decorated substrate is then recognized and degraded by the proteasome, a multi subunit protease.
  • Ub ligase E3 is the substrate recognition component of the ubiquitin system and carries out the rate-limiting step.
  • Fig. IB shows that VHL E3 normally does not recognize ERRa.
  • FIG. 1C describes a group of small molecules for VHL and ERRa exist.
  • Fig. ID shows a chimeric PROTAC adaptor can select endogenous ERRa for destruction by the VHL pathway.
  • the compound binds to both VHL and ERRa, bringing ERRa for VHL-mediated proteolysis.
  • Disclosed herein are much smaller moiety (i.e., Arg) for binding to a broadly expressed potent Ubrl E3, which leads to significant improvement.
  • Figs. 2A-2D show a number of small molecules synthesized.
  • Fig. 2A shows Arg linked to gefitinib, a drug for EGFR-dependent cancer.
  • Fig. 2B shows His linked to gefitinib.
  • Fig. 2C shows Arg linked to dasatinib, a drug for BCR-ABL dependent cancer.
  • Fig. 2D shows Arg linked to thiazolidinedione-based ligand for ERRa in breast cancer.
  • Figs. 3A-3C show that single amino acid based PROTACs induce ERRa turnover.
  • Fig. 3A shows that structure of PROTACs Arg-T ERRa and His-T ERRa . Arg and His were linked to the ligand previously demonstrated specifically for ERRa.
  • Fig. 3B shows that Arg-T ERRa and His-T ERRa trigger ERRa reduction in a dose-dependent manner. Varying amounts of Arg-T ERRa or His-T ERRa were added to MCF-7 cells. ERRoc levels were determined by western blot analysis. Equal amounts of protein extracts were used and ascertained by blotting with GAPDH antibody in the experiments. All experiments were done at least 3 times.
  • Fig. 3A shows that structure of PROTACs Arg-T ERRa and His-T ERRa . Arg and His were linked to the ligand previously demonstrated specifically for ERRa.
  • Fig. 3B shows that Arg-T ERRa and His-T
  • 3C shows that ERRoc stability was examined in the absence or presence of PROTACs by a protein expression shut-off assay.
  • MCF-7 cells with or without PROTACs were treated with 200 pg/ml cycloheximde to shut off protein synthesis.
  • Extracts were then collected at the indicated time points. Extracts were processed for
  • GAPDH serves as a loading control (lower panels).
  • Figs. 4A-4D show that ERRoc turnover is blocked by the inhibitors of the proteasome and the N-end rule pathway.
  • Fig. 4A and Fig. 4B show that ERRoc degradation involves the
  • MCF-7 cells were incubated with 10 mM Arg-T ERRa or 5 mM His-T ERRa for 32 h and then mixed with DMSO control or the proteasome inhibitor MG132 (25 mM).
  • ERRoc stability was determined after the addition of cycloheximde as described in Fig. 3C.
  • Fig. 4C and Fig. 4D show that Arg-T ERRa or His-T ERRa induced ERRoc reduction was reversed by dipeptides Arg-Ala and His-Ala, respectively.
  • MCF-7 cells incubated with 10mM Arg-T ERRa (Fig. 4C) or 5 mM His- T ERR a (Fig. 4D) were treated with dipeptides Arg-Ala (RA), His-Ala (HA) or control Ala- Ala (AA). Cell extracts were subjected to western blot analysis to determine the levels of ERRoc and control GAPDH.
  • Figs. 5A-5D show biological effects of Arg-T ERRa and His-T ERRa in MCF-7 cells.
  • Fig. 5A shows that PROTACs Arg- T ERRa and His-T ERRa inhibit breast cancer cell proliferation.
  • MCF-7 cells were treated with DMSO, 10 mM Arg-T ERRa or 5 mM His-T ERRa .
  • Cell proliferation was determined by the MTT assay after drug exposure on indicated days.
  • Fig. 5B shows that Arg-T ERRa and His-T ERRa impede wound healing.
  • Fig. 5C shows that Arg-T ERRa and His- T ERRa reduce breast cancer cell migration.
  • MCF-7 cells were allowed to invade transwell chambers for 48 h in the presence or absence of PROTACs. Invaded cells were then fixed, stained and photographed.
  • Fig. 5D shows effects of Arg-T ERRa and His-T ERRa on EMT markers.
  • cell extracts were analyzed by western blot to examine the expression of various EMT markers including fibronectin, N-cadherin, SNAIL and E- cadherin.
  • Figs. 6A-6B show single amino acid based PROTACs induce BCR-Abl turnover in K562 leukemia cells.
  • Fig. 6A shows the structure of PROTAC Arg-dasatinib. Arg was linked to the ligand dasatinib previously demonstrated specifically for Bcr-Abl, which triggers leukemia due to Philadephia chromosome translocation.
  • Fig. 6B shows that Arg-dasatinib induces BCR-ABL reduction in a dose-dependent manner. Varying amounts of Arg-dasatinib or control dasatinib were added to K562 cells for 24 hours. BCR-ABL 1 levels were determined by western blot analysis. Equal amounts of protein extracts were used and ascertained by blotting with tubulin antibody in the experiments. All experiments were done at least 3 times.
  • Fig. 7 shows synthesis of compound 1.3TFA (Arg-T ERRa in Fig. 3 A).
  • SI 1.0 equiv, 0.211 mmol, 100 mg
  • HATU 1.5 equiv, 0.316 mmol, 120 mg
  • DIPEA 1.5 equiv, 0.316 mmol, 52 pL
  • S2 1.1 equiv, 0.232 mmol, 23 mg
  • Fig. 8 shows the chemical structure of S3 in Fig. 7.
  • Fig. 9 shows the chemical structure of S5 in Fig. 7.
  • Fig. 10 shows the chemical structure of 1.3TFA in Fig. 7 (Arg-T ERRa in Fig. 3A).
  • Fig. 11 shows synthesis of compound 2.2 HCL (His-T ERRa in Fig. 3 A).
  • S2 1.1 equiv, 0.250 mmol, 25.0 mg
  • DCM 1.5 mL
  • S6 1.0 equiv, 0.227 mmol, 80.7 mg
  • HOBt 1.5 equiv, 0.340 mmol, 46.0 mg
  • DIPEA 3.0 equiv, 0.681 mmol, 112 pL
  • EDCI 1.5 equiv, 0.340 mmol, 65.2 mg.
  • the resulting solution was stirred at r.t. overnight.
  • DCM was removed.
  • the residue was diluted with H2O, and extracted with ethyl acetate.
  • the combined organic layers were washed with citric acid (aq., 2 M), brine, dried over Na2SC>4, filtered and concentrated in vacuo.
  • Fig. 12 shows the chemical structure of S8 in Fig. 11.
  • Fig. 13 shows the chemical structure of 2.2HCL (His-T ERRa in Fig. 3 A) in Fig. 11.
  • HRMS- ESI m/z: calc’d for C31H29F3N9O5S [M+H + ] 696.1959, found 696.1971.
  • the compound is represented by X-Y-Z (Formula I) or a pharmaceutically acceptable salt thereof; wherein X is a destabilization amino acid residue Y is a linker, and Z is a ligand that binds a receptor tyrosine kinase.
  • This compound and/or a pharmaceutical composition comprising this compound is useful for treating various cancers by degrading a receptor tyrosine kinase in the cancer cell.
  • an agonist includes a plurality of agonist, including mixtures thereof.
  • administering to a subject includes any route of introducing or delivering to a subject an agent. Administration can be carried out by any suitable route, including oral, topical, intravenous, subcutaneous, transcutaneous, transdermal, intramuscular, intra-joint, parenteral, intra-arteriole, intradermal, intraventricular, intracranial, intraperitoneal, intralesional, intranasal, rectal, vaginal, by inhalation or via an implanted reservoir, and the like. Administration includes self
  • compositions and methods include the recited elements, but not excluding others.
  • Consisting essentially of when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination. Thus, a composition consisting essentially of the elements as defined herein would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives, and the like.
  • Consisting of shall mean excluding more than trace elements of other ingredients and substantial method steps for administering the compositions of this invention. Embodiments defined by each of these transition terms are within the scope of this invention.
  • “Dysregulation” refers herein refers to an abnormal level of expression or activity of a protein or gene. This can include, for example, less levels or activities than in normal healthy humans. This can also include, for example, increased levels or activities than in normal healthy humans.
  • disclosed herein comprises a cancer results from a dysregulation of a receptor tyrosine kinase.
  • “Inhibit,” “inhibiting,” and “inhibition” mean to decrease an activity, response, condition, disease, or other biological parameter. This can include but is not limited to the complete ablation of the activity, response, condition, or disease. This may also include, for example, a 10% reduction in the activity, response, condition, or disease as compared to the native or control level. Thus, the reduction can be a 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels.
  • Ligand refers herein to a molecule that acts on a target in a desirable manner.
  • actions on a target in a desirable manner include, but are not limited to binding of the target, catalytically changing the target, reacting with the target in a way which modifies/alters the target or the functional activity of the target, covalently attaching to the target as in a suicide inhibitor, facilitating the reaction between the target and another molecule.
  • this desirable manner is binding to the target.
  • the ligand can be an organic compound or other chemical.
  • the ligand can be a compound, which is obtainable from or produced by any suitable source, whether natural or artificial.
  • the ligand can be an amino acid molecule, a polypeptide, a peptide or a chemical derivative thereof, or a combination thereof.
  • the ligand can also be a polynucleotide molecule - which can be a sense or an anti-sense molecule.
  • the ligand can even be an antibody.
  • the“ligand” refers to any ligand that binds to or be bound by a receptor tyrosine kinase.
  • the“ligand” refers to any ligand that binds to or be bound by a non-receptor tyrosine kinase
  • Tyrosine kinases herein refer to a family of enzymes that catalyze the phosphorylation of select tyrosine residues in the target proteins by using ATP.
  • Receptor tyrosine kinases or“RTKs” are used interchangeably herein to refer to a family of membrane receptors that phosphorylate tyrosine residues. Receptor tyrosine kinases possess an extracellular ligand binding domain, a transmembrane domain and an intracellular catalytic domain.
  • the extracellular domains bind cytokines, growth factors or other ligands and are generally comprised of one or more identifiable structural motifs, including cysteine-rich regions, fibronectin III- like domains, immunoglobulin- like domains, EGF-like domains, cadherin-like domains, kringle-like domains, Factor VIITlike domains, glycine-rich regions, leucine -rich regions, acidic regions and discoidin-like domains.
  • Activation of the intracellular kinase domain is achieved by ligand binding to the extracellular domain, which induces dimerization of the receptors.
  • a receptor activated in this way is able to autophosphorylate tyrosine residues outside the catalytic domain, facilitating stabilization of the active receptor conformation.
  • the phosphorylated residues also serve as binding sites for proteins which will then transduce signals within the cell.
  • Some RTKs are the high- affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer. Many play significant roles in development or cell division.
  • the RTK is estrogen-related receptor a.
  • the RTK is epidermal growth factor receptor.
  • “Non-receptor tyrosine kinases” refer to a second subgroup of tyrosine kinases that are cytosolic enzymes. Non-receptor tyrosine kinases relay intracellular signals originating from extracellular receptor.
  • the terms“prevent,”“preventing,”“prevention,” and grammatical variations thereof as used herein, refer to a method of partially or completely delaying or precluding the onset or recurrence of a disease and/or one or more of its attendant symptoms or barring a subject from acquiring or reacquiring a disease or reducing a subject’s risk of acquiring or reacquiring a disease or one or more of its attendant symptoms.
  • subject refers to a human in need of treatment for any purpose, and more preferably a human in need of treatment to treat a disease or disorder, such as a cancer.
  • subject can also refer to non-human animals, such as dogs, cats, horses, cows, pigs, sheep and non-human primates, among others.
  • “Pharmaceutically acceptable” component can refer to a component that is not biologically or otherwise undesirable, i.e., the component may be incorporated into a pharmaceutical formulation of the invention and administered to a subject as described herein without causing significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the formulation in which it is contained.
  • the term When used in reference to administration to a human, the term generally implies the component has met the required standards of toxicological and manufacturing testing or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration.
  • “Pharmaceutically acceptable carrier” means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non-toxic, and includes a carrier that is acceptable for veterinary and/or human
  • carrier or “pharmaceutically acceptable carrier” can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil/water or water/oil emulsion) and/or various types of wetting agents.
  • carrier encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in
  • compositions are pharmaceutical formulations.
  • choice of a carrier for use in a composition will depend upon the intended route of administration for the composition.
  • the preparation of pharmaceutically acceptable carriers and formulations containing these materials is described in, e.g., Remington's Pharmaceutical Sciences, 21st Edition, ed. University of the Sciences in Philadelphia, Lippincott, Williams & Wilkins, Philadelphia, PA, 2005.
  • physiologically acceptable carriers include saline, glycerol, DMSO, buffers such as phosphate buffers, citrate buffer, and buffers with other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEENTM (ICI, Inc.; Bridgewater, New Jersey), polyethylene glycol (PEG), and PLURONICSTM (BASF; Florham Park, NJ).
  • buffers such as phosphate buffer
  • “Pharmaceutically acceptable salt” as used herein refers to any salt that is pharmaceutically acceptable and has the desired pharmacological properties. Such salts are, for example, inorganic or organic base addition salts, or inorganic or organic acid addition salts. Each possibility represents a separate embodiment.
  • the terms“treating” or“treatment” of a subject includes the administration of a drug to a subject with the purpose of curing, healing, alleviating, relieving, altering, remedying, ameliorating, improving, stabilizing or affecting a disease or disorder, or a symptom of a disease or disorder.
  • the terms“treating” and“treatment” can also refer to reduction in severity and/or frequency of symptoms, elimination of symptoms and/or underlying cause, and improvement or remediation of damage.
  • “Therapeutic agent” refers to any composition that has a beneficial biological effect.
  • Beneficial biological effects include both therapeutic effects, e.g., treatment of a disorder or other undesirable physiological condition, and prophylactic effects, e.g., prevention of a disorder or other undesirable physiological condition (e.g., a cancer).
  • the terms also encompass pharmaceutically acceptable, pharmacologically active derivatives of beneficial agents specifically mentioned herein, including, but not limited to, salts, esters, amides, proagents, active metabolites, isomers, fragments, analogs, and the like.
  • therapeutic agent when used, then, or when a particular agent is specifically identified, it is to be understood that the term includes the agent per se as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, proagents, conjugates, active metabolites, isomers, fragments, analogs, etc.
  • “Therapeutically effective amount” or“therapeutically effective dose” of a composition refers to an amount that is effective to achieve a desired therapeutic result.
  • a desired therapeutic result is the treatment of a cancer.
  • a desired therapeutic result is the treatment of chronic myeloid leukemia, acute lymphocytic leukemia, breast cancer, or lung cancer.
  • Therapeutically effective amounts of a given therapeutic agent will typically vary with respect to factors such as the type and severity of the disorder or disease being treated and the age, gender, and weight of the subject.
  • the term can also refer to an amount of a therapeutic agent, or a rate of delivery of a therapeutic agent (e.g., amount over time), effective to facilitate a desired therapeutic effect, such as coughing relief.
  • a desired therapeutic effect will vary according to the condition to be treated, the tolerance of the subject, the agent and/or agent formulation to be administered (e.g., the potency of the therapeutic agent, the concentration of agent in the formulation, and the like), and a variety of other factors that are appreciated by those of ordinary skill in the art.
  • a desired biological or medical response is achieved following administration of multiple dosages of the composition to the subject over a period of days, weeks, or years.
  • X is a destabilization amino acid residue
  • Y is a linker
  • Z is a ligand that binds a tyrosine kinase
  • “Destabilization amino acid residue” is used herein to refer to an amino acid reside that can destabilize a protein if the amino acid residue is at the N-terminus, following the“N-end rule”.
  • the “N-end rule” states that the stability of a protein or a peptide is largely determined by the presence of“destabilizing” or“stabilizing” N-terminal amino acids.
  • the “N-end rule” states that the stability of a protein or a peptide is largely determined by the presence of“destabilizing” or“stabilizing” N-terminal amino acids.
  • destabilization amino acid residue can be, for example, Arg, His, Lys, Leu, lie, Phe, Trp, Tyr, Cys, Asn, Asp, Glu, or Gin.
  • the destabilization amino acid residue is Arg.
  • the destabilization amino acid residue is His. This single, destabilizing residue (e.g. Arg or His) at the N-terminus of a protein targets the substrate to a ubiquitin ligase termed Ubrl for rapid degradation via the N-end rule pathway.
  • Z is a ligand binds a receptor tyrosine kinase. In some embodiments, Z is a ligand binds a non-receptor tyrosine kinase.
  • the receptor tyrosine kinase described herein can be of any receptor tyrosine kinase.
  • the receptor tyrosine kinase comprises estrogen-related receptor a or epidermal growth factor receptor.
  • the receptor tyrosine kinase is estrogen-related receptor a.
  • the receptor tyrosine kinase is epidermal growth factor receptor.
  • the compound disclosed herein comprises a ligand binds estrogen-related receptor a.
  • the disclosed herein comprises a ligand binds epidermal growth factor receptor.
  • the non-receptor tyrosine kinase is Abelson tyrosine-protein kinase (ABL).
  • ABL Abelson tyrosine-protein kinase
  • the compound disclosed herein comprises a ligand that binds ABL.
  • the compound disclosed herein comprises a ligand that binds BCR- ABL fusion protein.
  • “Estrogen-related receptor a” or“ERR a” refers to estrogen-related receptor a polypeptide and, in humans, is encoded by the ESRRA gene.
  • the estrogen-related receptor a polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 3471, Entrez Gene: 2101, Ensembl: ENSG00000173153, OMIM: 601998, and UniProtKB: PI 1474.
  • the estrogen-related receptor a is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NO: l.
  • the estrogen-related receptor a is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:l. In some embodiments, the estrogen-related receptor a is a polypeptide comprising SEQ ID NO: 1.
  • “Epidermal growth factor receptor” or“EGFR” refers to epidermal growth factor receptor polypeptide and, in humans, is encoded by the EGFR gene.
  • the epidermal growth factor receptor polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 3236, Entrez Gene: 1956, Ensembl: ENSG00000146648, OMIM: 131550, or UniProtKB: P00533.
  • the epidermal growth factor is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NO: 2.
  • the epidermal growth factor is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:2. In some embodiments, the epidermal growth factor is a polypeptide comprising SEQ ID NO:2.
  • “Abelson tyrosine-protein kinase” or“ABL” refers to Abelson tyrosine-protein kinase polypeptide and, in humans, is encoded by the ABL1 gene.
  • the Abelson tyrosine-protein kinase polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 76, Entrez Gene: 25, Ensembl: ENSG00000097007,
  • the Abelson tyrosine-protein kinase is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NOG. In some embodiments, the Abelson tyrosine-protein kinase is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NOG. In some embodiments, the Abelson tyrosine-protein kinase is a polypeptide comprising SEQ ID NOG.
  • “Breakpoint cluster region protein” or“BCR” refers to breakpoint cluster region protein and, in humans, is encoded by the BCR gene.
  • the breakpoint cluster region polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 1014, Entrez Gene: 613, Ensembl: ENSG00000186716, OMIM: 151410, UniProtKB: PI 1274.
  • the breakpoint cluster region protein is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NO:4.
  • the breakpoint cluster region is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:4. In some embodiments, the breakpoint cluster region is a polypeptide comprising SEQ ID NO:4.
  • the ligand comprises an anti-cancer drug.
  • the anti-cancer drug can be any anti-cancer drug targeting a receptor tyrosine kinase (e.g., estrogen-related receptor a or epidermal growth factor receptor).
  • the anti-cancer drug includes, but not limited to, gefitinib, imatinib, erlotinib, sunitinib, lapatinib, trastuzumab, cetuximab, vercizumab, nilotinib, sorafenib, crizotinib, panitumumab, or a thiazolidinedione derivative.
  • the ligand is gefitinib.
  • the ligand is imatinib.
  • the anti-cancer drug can be any anti-cancer drug targeting a non-receptor tyrosine kinase (e.g., ABL).
  • the anti-cancer drug targets BCR- ABL fusion protein.
  • the ligand is dasatinib.
  • gefitinib The structure of gefitinib is shown below:
  • the ligand is a thiazolidinedione derivative.
  • the functional group of a thiazolidinedione is shown below:
  • the ligand is selected from the group consisting of pioglitazone, rosiglitazone, lobeglitazone, ciglitazone, garglitazone, englitazone, netoglitazone, rivoglitazone, troglitazone, and balaglitazone.
  • the thiazolidinedione derivative can be any thiazolidinedione derivative binding a receptor tyrosine kinase, including, for example, estrogen related receptor-a.
  • the thiazolidinedione derivative can be any one of the those disclosed in Application W02008109727A1, which is incorporated by reference herein in its entirety for its teaching of thiazolidinedione derivatives.
  • the thiazolidinedione derivative can be any one of the those disclosed in Application W02008109727A1, which is incorporated by reference herein in its entirety for its teaching of thiazolidinedione derivatives.
  • thiazolidinedione derivative has a formula (I)
  • Rl is halo, optionally substituted Ci-4alkyl, optionally substituted Ci-4alkoxy, or hydroxyl;
  • R2 is selected from halo substituted Ci-3alkyl, cyano, halo, -C(0)NH2, and -C(0)0-Ci-4alkyl, or alternatively R2 is linked together to R3 to form an aryl fused to the phenyl ring to which R2 and R3 are shown attached;
  • R3 is H, or alternatively R3 is linked together to R2 to form an aryl fused to the phenyl ring to which R3 and R2 are shown attached;
  • R4 is halo, cyano, -CoCH, halo substituted Ci-3alkyl, -C(0)0-Ci-4alkyl, -C(0)NH2, or -S(02)-Ci-4alkyl;
  • X is S or O; or an optical isomer, enantiomer, diastereomer, cis-
  • the linker (Y) comprises one or more covalently connected structural unit of A (e.g.,-Ai...A n -), wherein Ai is covalently linked to an X moiety and A n is covalently linked to a Z moiety, wherein the n is an integer greater than or equal to 0. In some embodiments, the n is greater than or equal to 1.
  • n is greater than 2
  • An is a group which is connected to a Z moiety
  • Ai and A n are connected via structural units of A (number of such structural units of A: n-2).
  • the q is 1, the structure of the linker group X is -Ai-, and Ai is a group which is connected to an X moiety and a Z moiety.
  • n is an integer from 1 to 100, 1 to 90, 1 to 80, 1 to 70, 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to 20, or 1 to 10.
  • Y can be absent (i.e., X moiety can be bound directly Z moiety). In other embodiments, Y is present.
  • the linking group can be any suitable group or moiety which is at minimum bivalent, and connects the heterocyclic rings in the nucleophile.
  • the linking group can be composed of any assembly of atoms, including oligomeric and polymeric chains. In some cases, the total number of atoms in the linking group can be from 3 to 200 atoms (e.g., from 3 to 150 atoms, from 3 to 100 atoms, from 3 and 50 atoms, from 3 to 25 atoms, from 3 to 15 atoms, or from 3 to 10 atoms).
  • the linking group can be, for example, an alkyl, alkoxy, alkylaryl, alkylheteroaryl, alkylcycloalkyl, alkylheterocycloalkyl, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, dialkylamino, alkylcarbonyl, alkoxycarbonyl,
  • alkylaminocarbonyl dialkylaminocarbonyl, or polyamino group.
  • the linking group can comprise one of the groups above joined to each of the heterocyclic rings by a functional group.
  • suitable functional groups include, for example, secondary amides (-CONH-), tertiary amides (-CONR-), secondary carbamates (-OCONH-; -NHCOO-), tertiary carbamates (-OCONR-; -NRCOO-), ureas (- NHCONH-; -NRCONH-; -NHCONR-, or -NRCONR-), carbinols ( -CHOH-, -CROH-), ethers (- 0-), and esters (-COO-, -CH2O2C-, CHRO2C-), wherein R is an alkyl group, an aryl group, or a heterocyclic group.
  • the linking group can comprise an alkyl group (e.g., a C1-C12 alkyl group, a Ci-Cs alkyl group, or a C1-C6 alkyl group) bound to each heterocyclic ring via an ester (-COO-, -CH2O2C-, CHRO2C-), a secondary amide (-CONH-), or a tertiary amide (-CONR-), wherein R is an alkyl group, an aryl group, or a heterocyclic group.
  • the linking group can also comprise a polyalkoxyl group (e.g., -polyethyloxy, polypropyloxy).
  • Y can be chosen from one of the following:
  • each m is, independent of any other, an integer from 1 to 12.
  • R 1 can be absent. In other embodiments, R 1 can be present. When present, R 1 can comprise a halogen, hydroxy, amino, cyano, azido, hydrazone, alkyl, alkenyl, alkynyl, alkoxy, aryl, heteroaryl, alkylaryl, alkylheteroaryl, cycloalkyl alky ley cloalkyl, heterocycloalkyl, alkylheterocycloalkyl, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, dialkylamino, alkylcarbonyl, alkoxycarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, peptidyl, polyamino, or polyalkyleneoxy group.
  • R 1 can comprise a cationic group.
  • the cationic group can comprise a cationic polyamino group (e.g., a polyethyleneimine segment).
  • the cationic group can comprise a cationic peptidyl group.
  • the cationic group can comprise a moiety (e.g., an alkyl group or an alkylaryl group) substituted with a cationic substituent, such as an ammonium group (e.g., a tetraalkylammonium group, an aryltrialkylammonium group, a diaryldialkylammonium group, or a
  • an ammonium group e.g., a tetraalkylammonium group, an aryltrialkylammonium group, a diaryldialkylammonium group, or a
  • R 1 can comprise a hydrophobic group.
  • R 1 can comprise an aryl group or an alkylaryl group.
  • R 1 can comprise a hydrophilic group.
  • R 1 can comprise a hydrophilic polyalkyleneoxy group (e.g., a polyethylene oxide segment).
  • R 1 can comprise a reactive functional group, such as an olefin, acetylene, alcohol, phenol, ether, oxide, halide, aldehyde, ketone, carboxylic acid, ester, amide, cyanate, isocyanate, thiocyanate, isothiocyanate, amine, hydrazine, hydrazone, hydrazide, diazo, diazonium, nitro, nitrile, mercaptan, sulfide, disulfide, sulfoxide, sulfone, sulfonic acid, sulfinic acid, acetal, ketal, anhydride, sulfate, sulfenic acid isonitrile, amidine, imide, imidate, nitrone, hydroxylamine, oxime, hydroxamic acid, thiohydroxamic acid, allene, ortho ester, sulfite, enamine
  • a reactive functional group such
  • the compound has a molecular weight no more than 2000 daltons, 1900 daltons, 1800 daltons, 1700 daltons, 1600 daltons, 1500 daltons, 1400 daltons, 1300 daltons, 1200 daltons, 1100 daltons, 1000 daltons, 990 daltons, 980 daltons, 970 daltons, 960 daltons, 950 daltons, 940 daltons, 930 daltons, 930 daltons, 920 daltons, 910 daltons, 900 daltons, 890 daltons, 880 daltons, 870 daltons, 860 daltons, 850 daltons, 840 daltons, 830 daltons, 820 daltons, 810 daltons, 800 daltons, 790 daltons, 780 daltons, 770 daltons, 760 daltons, 750 daltons, 740 daltons, 730 daltons, 720 daltons, 7
  • the compound is selected from the group consisting of:
  • composition comprising the compound any preceding aspect, and a pharmaceutically acceptable carrier.
  • a method for treating a cancer in a subject in need thereof comprising: administering a therapeutically effective amount of a compound of Formula I:
  • X is a destabilization amino acid residue
  • Y is a linker
  • Z is a ligand that binds a tyrosine kinase
  • the cancer results from a dysregulation of the tyrosine kinase.
  • “Dysregulation” refers herein refers to an abnormal level of expression or activity of a protein or gene. This can include, for example, less levels or activities than in normal healthy humans. This can also include, for example, increased levels or activities than in normal healthy humans.
  • disclosed herein comprises a cancer results from a dysregulation of a receptor tyrosine kinase (e.g., estrogen-related receptor a or epidermal growth factor receptor) and/or a non receptor tyrosine kinase (e.g., ABL).
  • a receptor tyrosine kinase e.g., estrogen-related receptor a or epidermal growth factor receptor
  • ABL non receptor tyrosine kinase
  • the present invention encompasses a method for treating any cancer having a dysregulation of the receptor tyrosine kinase and/or a non-receptor tyrosine kinase.
  • cancer can be, for example, lymphoma, B cell lymphoma, T cell lymphoma, mycosis fungoides, Hodgkin’s Disease, myeloid leukemia, bladder cancer, brain cancer, nervous system cancer, head and neck cancer, squamous cell carcinoma of head and neck, lung cancers such as small cell lung cancer and non-small cell lung cancer, neuroblastoma/glioblastoma, ovarian cancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas of the mouth, throat, larynx, and lung, cervical cancer, cervical carcinoma, breast cancer, and epithelial cancer, renal cancer, genitourinary cancer, pulmonary cancer, esophageal carcinoma, head and neck carcinoma, large bowel cancer, hematopoi
  • the cancer is chronic myeloid leukemia. In some embodiments, the cancer is acute lymphocytic leukemia. In some embodiments, the cancer is breast cancer. In some embodiments, the cancer is lung cancer. In some embodiments, the cancer is kidney cancer.
  • the subject is a human.
  • the human has a cancer.
  • the human is suspected to have a cancer.
  • Dosing frequency for the compound includes, but is not limited to, at least about once every 12 months, once every 11 months, one every 10 months, once every 9 months, once every 8 months, once every 7 months, once every 6 months, once every 5 months once every 4 months, once every once every 3 months, once every 12 weeks, once every 10 weeks, once every 8 weeks, once every 7 weeks, once every 6 weeks, once every 5 weeks, once every 4 weeks, once every 3 weeks, once every 2 weeks, or weekly.
  • the dosing frequency for the compound can be, for example, about once every 10 days, once every 9 days, once every 8 days, once every 7 days, once every 6 days, once every 5 days, once every 4 days, once every 3 days, once every 2 days, once every day, two times a day, three times a day, four times a day, five times a day, or six times a day.
  • the interval between each administration is less than about a week, such as less than about any of 6, 5, 4, 3, 2, or 1 day.
  • the interval between each administration can be more than a week, such as, more than two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, ten weeks, eleven weeks, twelve weeks, three months, four months, five months, or six months.
  • a week such as, more than two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, ten weeks, eleven weeks, twelve weeks, three months, four months, five months, or six months.
  • the interval between each administration is constant.
  • Administration can also be continuous and adjusted to maintaining a level of the compound within any desired and specified range.
  • the MCF-7 cell line (ATCC, Manassas, VA) was maintained at 37°C with 5% CO2 in DMEM with 2 mM L-glutamine that was modified to contain 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, and 1.5 g/1 sodium bicarbonate. It was also supplemented with 10% fetal bovine serum, 10 pg/ml bovine insulin, 100 units/pl penicillin/streptomycin. All drug treatment study was supplemented with 2% FBS. Functional assays including MTT, migration assays were done in 10% FBS in DMEM media
  • MCF-7 cells (lxlO 4 ) were seeded on an 8 mM pore size Thin-cert for 24 well plates (Greiner Bio-One) in serum free media.
  • PROTAC compounds were added to the bottom chamber as chemoattractant.
  • cells on the top of the membrane were removed with a cotton swab.
  • the migrated cells at the bottom side were washed with PBS, fixed with 70% ethanol and stained using 0.1% Crystal violet to visualize the migrated cells.
  • Migrated cells attached to the lower side of the membrane were enumerated using a light microscope at lOx magnification.
  • a short binding motif to a potent ubiquitin ligase can greatly improve the utility of the PROTAC approach.
  • the shortest degradation motif is single amino acid, a destabilizing residue (e.g., Arg, His, Lys, Leu, lie) at the N-terminus of a protein that targets the substrate to a ubiquitin ligase termed Ubrl for rapid degradation via N-end rule pathway, the first ubiquitin dependent degradation pathway identified.
  • Ubrl is constitutive active and broadly expressed, making it ideally suited for this strategy.
  • Adaptor molecules were synthesized starting with Arg and fused to a variety of cancer drugs.
  • Arg was appended to imatinib, a moiety specific for BCR-ABL protein.
  • imatinib a moiety specific for BCR-ABL protein.
  • the synthetic molecule can markedly reduce BCR-ABL level, which is key to chronic myeloid leukemia (CML) and acute lymphocytic leukemia (ALL). Improvements over existing strategies were achieved including: i) a small ubiquitin ligase-binding motif (i.e.
  • Arg markedly reducing the size of an adaptor, which increases cell permeability and efficacy; ii) the employment of Ubrl, a broadly expressed, potent ubiquitin ligase; iii) the Arg residue can be easily replaced with others (e.g. Lys, His) that changes the degradation speed due to different affinity for Ubrl, allowing optimal modulation of protein stability.
  • Adaptor molecules were synthesized starting with Arg or His and fused to a ligand for estrogen-related receptora (ERRa) (Fig. 1 A), a nuclear receptor that is a major regulator of several critical metabolic pathways and also is a prognostic marker of breast cancer.
  • ERRa inhibition has been shown to reduce the proliferation of breast tumor cells in vitro and in vivo. It was found that both compounds reduced endogenous ERRa level in the MCF-7 metastatic breast cancer cell line (Fig. IB and Fig. 1C). To assess whether ERRa decrease was due to protein turnover, the cells were treated with cycloheximide to block protein synthesis and collected the samples at various time points for western blotting analysis. Both of these compounds triggered ERRa degradation (Fig. ID).
  • fusion molecules were synthesized (Figs. 2A-2D) derived from gefitinib to target EGFR in lung cancer cells (H1299, H1975, HCC827, H3255), imatinib and dasatinib to target BCR-ABL protein in leukemia cells (e.g., K562, EM3, NAML1, KCL22, LAMA84, SUP- B15), and thiazolidinedione-based ligand for ERRa in breast cancer cells (e.g., MCF7, MDA-MB- 231).
  • leukemia cells e.g., K562, EM3, NAML1, KCL22, LAMA84, SUP- B15
  • thiazolidinedione-based ligand for ERRa in breast cancer cells e.g., MCF7, MDA-MB- 231).
  • the drugs e.g., gefitinib, imatinib, dasatinib
  • the drugs have been previously analyzed and are effective in target inhibition albeit resistance often occurs later developed.
  • these novel Arg- based molecules more molecules using chemical mimics of Arg are generated.
  • the capacity of these fusion molecules e.g., Arg-gefitinib chimera
  • targets e.g., EGFR, BCR-ABL, ERRa
  • their physiological effects e.g., cell proliferation, receptor signaling, apoptosis
  • their efficacy in mouse xenograft models, and ultimately in affected leukemia patients are evaluated.
  • FIG. 3A The chemical structure of an example of adaptor molecules synthesized starting with Arg or His and fused to a ligand for estrogen-related receptor a (ERRa) was shown (Fig. 3A), as introduced above (Figs. 1A-1D). It was shown herein that both compounds Arg-T ERRa and His- T ERRa reduced endogenous ERRa level in the MCF-7 metastatic breast cancer cell line (Fig. 3B).
  • EMT epithelial- mesenchymal transition
  • the advantage of this approach lies in the use of the simplest degradation signal - single amino acid, which can be any one of the thirteen destabilizing residues in the N-end rule pathway that in turn can lead to different degradation speed.
  • the PROTAC method presented here overcomes limitations of existing approaches with significantly smaller molecular size of E3 targeting moiety, leading to higher permeability and better efficacy, and a modulatable potent degradation activity, allowing better control and broader application.
  • the N-end rule degradation pathway is universally present and constitutively active, making it ideally suited for the PROTAC approach. This modular design expands the repertoire of limited ubiquitin pathways currently available for PROTACs and can be easily adapted for broad use in targeted protein degradation.
  • Arg-T ERRa and His-T ERRa syntheses are described in Figs. 7-10 and Figs. 11-13, respectively.
  • Dipeptides Arg-Ala and His-Ala were purchased from Bachem Americas (Torrance, CA).
  • MG132 is a proteasome inhibitor obtained from Calbiochem (Gibbstown, NJ).
  • Cyclohexamide was purchased from Sigma-Aldrich (Saint Louis, MO).
  • Yields refer to chromatographically. Reagents were purchased at the highest commercial quality and used without further purification, unless otherwise stated.
  • NMR spectra were recorded on Briiker Advance 500 (1H 500 MHz, 13C 125 MHz) and Briiker Advance 400 (1H 400 MHz, 13C 100 MHz) and are calibrated using residual undeuterated solvent (CDC13 at 7.26 ppm 1H NMR, 77.16 ppm 13C NMR; pyridine-d5 at 8.70 ppm 1H NMR, 149.6 ppm 13C NMR).
  • Mass spectrometric data were obtained using Briiker Apex IV FTMS using ESI (electrospray ionization) and Waters GCT (GC-MS) using El (electron impact ionization).

Abstract

Disclosed are compounds that target receptor tyrosine kinases for degradation by ubiquitinases, and the use thereof for treating cancers.

Description

COMPOSITIONS AND METHODS FOR CANCER THERAPY
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of priority to U.S. Provisional Patent Application No. 62/871,516, filed July 8, 2019, the disclosure of which is expressly incorporated herein by reference.
STATEMENT REGARDING GOVERNMENT SUPPORT
[0002] This invention was made with government support under grant no. UL1TR001120 awarded by the National Center for Advancing Translational Science. The government has certain rights in the invention.
FIELD
[0003] The present disclosure relates to compositions and methods for treating cancers.
BACKGROUND
[0004] Ligand-induced selective proteolysis has emerged as a promising therapeutic means for cancer. For example, AS2O3 triggers proteasome-mediated degradation of PML and retinoic acid receptor, which is the basis of its clinical efficacy in acute promyelocytic leukemia. Harnessing the power of the proteolytic system to degrade proteins for therapeutic benefit has been under exploration. Zhou and Howley were the first to rewire the ubiquitin-proteasome pathway, a major degradation system for selective proteolysis, to degrade normally stable proteins in vivo (e.g., yeast). The principle of protein knockdown strategy is based on ubiquitin-mediated proteolysis (Fig. 1A); a ubiquitin ligase (E3) recognizes its target and covalently attaches ubiquitin, a conserved 76-residue protein, onto the substrate, leading to subsequent degradation by the proteasome, a multi-subunit protease. In the last about 18 years, a number of groups manipulated different components involved in protein knockdown and demonstrated their utility mainly in tissue culture-based experiments, but largely failed to adapt the strategy in therapeutic relevant physiological settings (e.g., mouse models). The challenges encountered include poor target specificity, low cellular potency and alteration of critical cellular systems with undesirable side effects.
[0005] Recently, a group of small molecules were developed to efficiently knock down estrogen- related receptor a (ERRa), a key player in breast cancer, and led to tumor regression in the mouse model. In this PROTAC (proteolysis targeting chimera) approach, the small molecule is composed of a ligand for the target protein and a moiety that binds a ubiquitin ligase, which can trigger target destruction. To eliminate ERRa, an adapter molecule was designed to bring ERRa to a ubiquitin ligase E3 (i.e., VHL) for destruction in mammalian cells and mouse xenograft models (Figs. IB ID). The study overcame a major roadblock in the therapeutic potential of protein knockdown approach.
[0006] The PROTAC approach tackles two major issues in drug therapy: i) drug resistance.
Resistance often arises when tumors adapt to the drug and manage to find alternate routes to resume cell growth. A major reason behind the acquired resistance, a problem plaguing many inhibitor-based therapies, is that drug inhibition requires persistent binding of the drug and target, which provides time for cells to develop alternative routes (e.g., secondary mutations) to resume cell growth. The PROTAC adds a degradation signal that rapidly destroys the target, thereby limiting the time of drug engagement and reducing the risk that acquired defects accumulate and phenotypes are reversed ii) difficulty in monitoring and/or blocking target activity. Many cancer targets don’t have obvious enzymatic activity (e.g., kinase) that could be easily assayed in vivo and in vitro, making it hard to monitor the effects of inhibitors. In addition, whereas the molecules binding to the targets are not difficult to obtain, many of these molecules do not block the target activity. The PROTAC requires neither the direct inhibition of target activity nor the stable drug- target interaction since the target would be destroyed on contact upon drug exposure. Therefore, the PROTAC can be used on any molecule that can recognize relevant disease targets via the appendage of additional degradation moiety.
[0007] Of the two main components of the PROTAC, while the ligands for various targets have been developed and refined over the years, the degradation motifs used currently remain underdeveloped. Thus far, degradation moieties specific for a few ubiquitin ligases (e.g., VHL, cereblon, MDM2, XIAP) have been validated for triggering destruction of a variety of key cancer proteins and successfully demonstrated in mouse models for cancer (e.g., breast cancer and leukemia). However, these ubiquitin ligases (e.g., Cereblon and VHL) may not be easily adopted for other cancers, such as, brain cancer, lung cancer and kidney cancer, due to their low
expression/activity in these cells. Another caveat with the degradation motifs employed is lack of degradation speed control, which can be a problem as too much or fast substrate turnover may be harmful in some cases. Moreover, it is important to reduce the sizes of PROTACs that currently are much larger than typical drugs (often less than 500 daltons), which could improve cellular permeability and potency. Therefore, what is needed is novel PROTAC molecules with reduced sizes and therapeutic methods that are more generally applicable for various cancers. The compositions and methods disclosed herein address these and other needs. SUMMARY
[0008] In accordance with the purposes of the disclosed materials and methods, as embodied and broadly described herein, the disclosed subject matter, in one aspect, relates to compounds, compositions and methods of making and using compounds and compositions.
[0009] The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.
[0010] In some aspects, disclosed herein is a compound of Formula I:
X-Y-Z
Formula I wherein:
X is a destabilization amino acid residue;
Y is a linker; and
Z is a ligand that binds a tyrosine kinase;
or a pharmaceutically acceptable salt thereof.
[0011] In some embodiment, the destabilization amino acid residue is selected from the group consisting of Arg, His, Lys, Leu, lie, Phe, Trp, Tyr, Cys, Asn, Asp, Glu, and Gin.
[0012] In some embodiments, the destabilization amino acid residue is Arg or His.
[0013] In some embodiments, the tyrosine kinase is a receptor tyrosine kinase or a non-receptor tyrosine kinase. In some embodiments, the receptor tyrosine kinase comprises estrogen-related receptor a or epidermal growth factor receptor.
[0014] In some embodiments, the ligand comprises an anti-cancer drug. In some embodiments, the anti-cancer drug comprises gefitinib, dasatinib, imatinib, crizotinib, lapatinib, or a thiazolidinedione derivative.
[0015] In some embodiments, the compound has a molecular weight no more than 1000 daltons.
[0016] In some embodiments, the compound is selected from the group consisting of
Figure imgf000004_0001
Figure imgf000005_0001
[0017] In some aspects, disclosed herein is a pharmaceutical composition, comprising: the compound of any preceding aspect; and a pharmaceutically acceptable carrier.
[0018] In some aspects, disclosed herein is a method for treating a cancer in a subject in need thereof, comprising: administering a therapeutically effective amount of the pharmaceutical composition of any preceding aspect. In some embodiments, the cancer comprises chronic myeloid leukemia, acute lymphocytic leukemia, breast cancer, or lung cancer. In some embodiments, the subject is a human.
[0019] In some aspects, disclosed herein is a method of treating a cancer in a subject in need thereof, comprising: administering a therapeutically effective amount of a compound of Formula I:
X-Y-Z
Formula I wherein:
X is a destabilization amino acid residue;
Y is a linker; and
Z is a ligand that binds a tyrosine kinase;
or a pharmaceutically acceptable salt thereof.
[0020] Additional advantages will be set forth in part in the description that follows, and in part will be obvious from the description, or may be learned by practice of the aspects described below. The advantages described below will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive.
BRIEF DESCRIPTION OF DRAWINGS
[0021] The accompanying figures, which are incorporated in and constitute a part of this specification, illustrate several aspects described below.
[0022] Figs. 1A-1D show targeting estrogen-related receptor a (ERRa) for destruction. Fig. 1A shows that in ubiquitin (Ub)-mediated degradation, a Ub ligase E3 binds the substrate and put on a chain of Ub molecules (red dots), a molecular marker for the proteasome, with the help of El and E2 enzymes. Ub-decorated substrate is then recognized and degraded by the proteasome, a multi subunit protease. Ub ligase E3 is the substrate recognition component of the ubiquitin system and carries out the rate-limiting step. Fig. IB shows that VHL E3 normally does not recognize ERRa. Fig. 1C describes a group of small molecules for VHL and ERRa exist. Fig. ID shows a chimeric PROTAC adaptor can select endogenous ERRa for destruction by the VHL pathway. The compound binds to both VHL and ERRa, bringing ERRa for VHL-mediated proteolysis. Disclosed herein are much smaller moiety (i.e., Arg) for binding to a broadly expressed potent Ubrl E3, which leads to significant improvement.
[0023] Figs. 2A-2D show a number of small molecules synthesized. Fig. 2A shows Arg linked to gefitinib, a drug for EGFR-dependent cancer. Fig. 2B shows His linked to gefitinib. Fig. 2C shows Arg linked to dasatinib, a drug for BCR-ABL dependent cancer. Fig. 2D shows Arg linked to thiazolidinedione-based ligand for ERRa in breast cancer.
[0024] Figs. 3A-3C show that single amino acid based PROTACs induce ERRa turnover. Fig. 3A shows that structure of PROTACs Arg-TERRa and His-TERRa. Arg and His were linked to the ligand previously demonstrated specifically for ERRa. Fig. 3B shows that Arg-TERRa and His-TERRa trigger ERRa reduction in a dose-dependent manner. Varying amounts of Arg-TERRa or His-TERRa were added to MCF-7 cells. ERRoc levels were determined by western blot analysis. Equal amounts of protein extracts were used and ascertained by blotting with GAPDH antibody in the experiments. All experiments were done at least 3 times. Fig. 3C shows that ERRoc stability was examined in the absence or presence of PROTACs by a protein expression shut-off assay. MCF-7 cells with or without PROTACs were treated with 200 pg/ml cycloheximde to shut off protein synthesis.
Samples were then collected at the indicated time points. Extracts were processed for
immunoblotting with ERRoc antibody. GAPDH serves as a loading control (lower panels).
[0025] Figs. 4A-4D show that ERRoc turnover is blocked by the inhibitors of the proteasome and the N-end rule pathway. Fig. 4A and Fig. 4B show that ERRoc degradation involves the
proteasome. MCF-7 cells were incubated with 10 mM Arg-TERRa or 5 mM His-TERRa for 32 h and then mixed with DMSO control or the proteasome inhibitor MG132 (25 mM). ERRoc stability was determined after the addition of cycloheximde as described in Fig. 3C. Fig. 4C and Fig. 4D show that Arg-TERRa or His-TERRa induced ERRoc reduction was reversed by dipeptides Arg-Ala and His-Ala, respectively. MCF-7 cells incubated with 10mM Arg-TERRa (Fig. 4C) or 5 mM His- TERRa (Fig. 4D) were treated with dipeptides Arg-Ala (RA), His-Ala (HA) or control Ala- Ala (AA). Cell extracts were subjected to western blot analysis to determine the levels of ERRoc and control GAPDH.
[0026] Figs. 5A-5D show biological effects of Arg-TERRa and His-TERRa in MCF-7 cells. Fig. 5A shows that PROTACs Arg- TERRa and His-TERRa inhibit breast cancer cell proliferation. MCF-7 cells were treated with DMSO, 10 mM Arg-TERRa or 5 mM His-TERRa. Cell proliferation was determined by the MTT assay after drug exposure on indicated days. Fig. 5B shows that Arg-TERRa and His-TERRa impede wound healing. Confluent monolayers of MCF-7 cells were scraped by a pipette tip to generate wounds and then treated with DMSO, 10 mM Arg-TERRa or 5 mM His-TERRa. Wound repair was photographed at indicated time points. Fig. 5C shows that Arg-TERRa and His- TERRa reduce breast cancer cell migration. MCF-7 cells were allowed to invade transwell chambers for 48 h in the presence or absence of PROTACs. Invaded cells were then fixed, stained and photographed. Fig. 5D shows effects of Arg-TERRa and His-TERRa on EMT markers. After the exposure to 10 mM Arg-TERRa or 5 mM His-TERRa, cell extracts were analyzed by western blot to examine the expression of various EMT markers including fibronectin, N-cadherin, SNAIL and E- cadherin.
[0027] Figs. 6A-6B show single amino acid based PROTACs induce BCR-Abl turnover in K562 leukemia cells. Fig. 6A shows the structure of PROTAC Arg-dasatinib. Arg was linked to the ligand dasatinib previously demonstrated specifically for Bcr-Abl, which triggers leukemia due to Philadephia chromosome translocation. Fig. 6B shows that Arg-dasatinib induces BCR-ABL reduction in a dose-dependent manner. Varying amounts of Arg-dasatinib or control dasatinib were added to K562 cells for 24 hours. BCR-ABL 1 levels were determined by western blot analysis. Equal amounts of protein extracts were used and ascertained by blotting with tubulin antibody in the experiments. All experiments were done at least 3 times.
[0028] Fig. 7 shows synthesis of compound 1.3TFA (Arg-TERRain Fig. 3 A). To a solution of SI (1.0 equiv, 0.211 mmol, 100 mg) in THF (1 mL) was added HATU (1.5 equiv, 0.316 mmol, 120 mg), DIPEA (1.5 equiv, 0.316 mmol, 52 pL) and S2 (1.1 equiv, 0.232 mmol, 23 mg). The resulting solution was stirred at r.t. overnight. After the starting material S 1 was completely consumed (monitored by TLC), THF was removed and the residue was purified by flash column
chromatography to give the desired product S3 (106 mg, 90% yield) as a colorless oil. To a solution of S3 (1.24 equiv, 0.144 mmol, 80 mg) and S4 (1.0 equiv, 0.116 mmol, 53 mg) in THF (3 mL) was added CuTC (0.14 equiv, 0.016 mmol, 3 mg). The resulting mixture was stirred at r.t. overnight, then THF was removed and the residue was purified by flash column chromatography to give product S5 (49 mg, 42% yield) as a white solid. To a solution of S5 (0.018 mmol, 18.5 mg) in DCM (0.5 mL) was added TFA (0.5 mL). The resulting solution was stirred at r.t. for 1 h. Then the solution was concentrated in vacuo to afford 1 as a white solid (17.3 mg, 82% yield), which was used directly in the biological tests without further purification.
[0029] Fig. 8 shows the chemical structure of S3 in Fig. 7. Rf = 0.5 (EtOAc : PE = 1 : 1); HRMS- ESI (m/z) calc for C24H45N8O7 [M+H+] 557.3406, found 557.3404, found 557.3404; ¾ NMR (400 MHz, CDCL): d 9.40-9.32 (m, 2H), 7.14 (brs, 1H), 5.98 (d, J = 8.8 Hz, 1H), 4.32-4.27 (m, 1H), 4.00-3.94 (m, 1H), 3.71-3.63 (m, 1H), 3.43-3.37 (m, 1H), 3.31 (t, J = 6.7 Hz, 2H), 3.27-3.21 (m, 1H), 1.87-1.66 (m, 6H), 1.51 (s, 18H), 1.44 (s, 9H); 13C NMR (125 MHz, CDCL) d 172.56, 163.17, 160.97, 155.76, 154.93, 84.43, 79.86,79.63, 53.95, 49.32, 44.12, 37.11, 29.06, 28.66, 28.58, 28.39, 28.16, 24.70.
[0030] Fig. 9 shows the chemical structure of S5 in Fig. 7. Rf = 0.4 (EtOAc : PE = 3:1); HRMS- ESI (m/z): calc’d for C46H58F3N10O11S [M+H+] 1015.3954, found 1015.3924; ¾ NMR (400 MHz, CDC13): d 9.36-9.31 (m, 2H), 7.96 (s, 1H), 7.88 (s, 1H), 7.74 (s, 1H), 7.67 (d, J = 8.7 Hz, 1H),7.22- 7.15 (m, 3H), 7.12 (s, 1H), 6.76 (d, J = 8.7 Hz, 1H), 5.98 (d, J = 8.4 Hz, 1H), 5.04 (s,2H), 4.34 (t, J = 6.8 Hz, 2H), 4.31-4.27 (m, 1H), 3.98-3.92 (m, 1H), 3.80 (s, 3H), 3.72-3.62(m, 1H), 3.39-3.31 (m, 1H), 3.23-3.18 (m, 1H), 2.13-2.06 (m, 2H), 1.89-1.73 (m,4H), 1.51(s, 9H), 1.46 (s, 9H), 1.44 (s, 9H); 13C NMR (150 MHz, CDCL) d 172.92, 166.95, 165.53, 163.17, 160.96, 159.01,
155.71,154.85, 151.83, 143.57, 141.32, 137.16, 132.93, 132.51, 131.69 (q, 7 = 4.9 Hz), 123.80,123.30, 122.29 (q, 7 = 273.3 Hz), 122.22, 120.56 (q, J = 32.9 Hz), 117.57, 116.61,
114.51,105.95, 84.32, 79.89, 79.42, 56.20, 53.96, 47.89, 43.94, 36.78, 36.51, 30.51, 28.49, 28.33,28.08, 24.64; 19F NMR (565 MHz, CDCh) d -62.74.
[0031] Fig. 10 shows the chemical structure of 1.3TFA in Fig. 7 (Arg-TERRain Fig. 3A). HRMS- ESI (m/z): calc’d for C31H34F3N10O5S [M+H+] 715.2381, found 715.2399.1H NMR (400 MHz, DMSO): d 8.61 (t, J = 5.6 Hz, 1H), 8.34 (d, J = 2.0 Hz, 1H), 8.19-8.17 (d, J = 5.0 Hz, 3H), 8.15 (s, 1H), 8.04-8.01 (m, 2H), 7.75 (t, J = 5.5 Hz, 1H), 7.55 (d, J = 2.0 Hz, 1H), 7.40 (d, J = 8.3 Hz, 1H),7.31 (dd, J = 8.4, 2.0 Hz, 1H), 6.93 (d, J = 8.8 Hz, 1H), 4.92 (s, 2H), 4.38 (t, J = 7.0 Hz,2H), 3.80 (s, 3H), 3.74-3.70 (m, 1H), 3.16-3.09 (m, 4H), 2.02-1.94 (m, 2H), 1.72-1.66 (m,2H), 1.51- 1.43(m, 2H).13C NMR (150 MHz, DMSO) d 168.57, 166.89, 165.17, 158.79 (q, J = 36.0 Hz), 158.43,156.97, 151.34, 142.92, 141.05, 138.79, 132.65, 132.30, 132.03,123.81, 123.12,
122.98,122.55 (q, J = 273.6 Hz), 121.76, 118.70 (q, J = 31.9 Hz), 117.59, 117.07, 116.06, 115.91(q, 7 = 290.5 Hz), 105.44, 56.23,52.13, 47.20, 40.17, 36.80, 36.07, 29.69, 28.33, 24.33. 19F NMR (565 MHz, DMSO) d -61.22, -74.80.
[0032] Fig. 11 shows synthesis of compound 2.2 HCL (His-TERRain Fig. 3 A). To a solution of S2 (1.1 equiv, 0.250 mmol, 25.0 mg) in DCM (1.5 mL) was added S6 (1.0 equiv, 0.227 mmol, 80.7 mg), HOBt (1.5 equiv, 0.340 mmol, 46.0 mg), DIPEA (3.0 equiv, 0.681 mmol, 112 pL) and EDCI (1.5 equiv, 0.340 mmol, 65.2 mg). The resulting solution was stirred at r.t. overnight. After the starting material S6 was completely consumed (monitored by TLC), DCM was removed. The residue was diluted with H2O, and extracted with ethyl acetate. The combined organic layers were washed with citric acid (aq., 2 M), brine, dried over Na2SC>4, filtered and concentrated in vacuo.
The crude product S7 (white solid, 57.8 mg) was used immediately in the next step without purification. To a solution of S7 (1.0 equiv, 0.132 mmol, 57.8 mg) and S4 (1.0 equiv, 0.132 mmol, 60.6 mg) in THF (3.5 mL) was added CuTC (0.1 equiv, 0.013 mmol, 2.5 mg). The resulting mixture was stirred at r.t. overnight, then THF was removed and the residue was purified by flash column chromatography to give product S8 (84.1 mg, 41% yield for 2 steps) as a white solid.
Compound S8 (0.036 mmol, 32.4 mg) was dissolved in a solution of HC1 in MeOH (0.5 M, 4 mL). The resulting solution was stirred at r.t. for 2 h. Then the solution was concentrated in vacuo to afford 2 as a yellow solid (30.5 mg, quant.), which was used directly in the biological tests without further purification.
[0033] Fig. 12 shows the chemical structure of S8 in Fig. 11. Rf = 0.1 (EtOAc: PE =3:1) HRMS- ESI (m/z): calc’d for C41H45F3N9O9S [M+H+] 896.3008, found 896.2998. Ή NMR (400 MHz, CDCL): d 8.01 (brs, 1H), 7.94 (s, 1H), 7.86 (s, 1H), 7.74 (s, 1H), 7.66 (dd, J = 8.6, 1.4 Hz, 1H), 7.20-7.09 (m, 5H), 6.76 (d, 7 = 8.7 Hz, 1H), 6.10 (brs, 1H), 5.02 (s, 2H), 4.39 (brs, 1H), 4.31-4.27 (m, 2H), 3.79 (s, 3H), 3.28-3.18 (m, 2H), 3.06-2.93 (m, 2H), 2.08-1.99 (m, 2H), 1.56 (s, 9H), 1.40 (s, 9H). 13C NMR (125 MHz, CDC13) d 172.07, 166.94, 165.54, 159.03, 151.87, 143.67,
141.34,137.15, 132.92, 132.54, 131.70 (q, 7 = 5.1 Hz), 123.87, 123.83, 123.28, 122.32 (q, 7 =273.3 Hz), 122.26, 120.64 (q, 7 = 32.9 Hz), 117.54, 116.67, 114.62, 106.02, 85.98, 80.17,56.25, 47.50, 36.81, 36.17, 30.29, 28.38, 27.92. 19F NMR (471 MHz, CDC1 ) d -62.72.
[0034] Fig. 13 shows the chemical structure of 2.2HCL (His-TERRain Fig. 3 A) in Fig. 11. HRMS- ESI (m/z): calc’d for C31H29F3N9O5S [M+H+] 696.1959, found 696.1971. ¾ NMR (400 MHz, CD30D): d 8.94 (s, 1H),8.23 (brs, 1H), 8.11 (s, 1H), 7.98 (s, 1H), 7.85 (d, 7 = 8.1 Hz, 1H), 7.55 (s, 1H), 7.37 (s, 1H), 7.3 l(s, 2H), 6.87 (d, J = 8.7 Hz, 1H), 5.05 (s, 2H), 4.49-4.46 (m, 2H), 4.29-4.26 (m, 1H), 3.82 (s, 3H), 3.44-3.20 (m, 4H), 2.13 (brs, 2H). 13C NMR (125 MHz, CD3OD) d 168.66, 168.39, 166.75, 160.32, 153.13, 144.77, 139.04, 135.98, 134.18, 133.94, 132.67 (q, 7 = 5.1 Hz), 128.21, 124.64, 124.25, 123.85 (q, 7 = 272.9 Hz), 123.22, 121.06 (q, 7 = 32.4 Hz), 119.91, 118.43, 118.02, 116.45, 106.97, 56.88, 53.54, 49.91, 37.70, 36.90, 30.59, 27.74. 19F NMR (471 MHz, CD3OD) d -63.91.
DETAILED DESCRIPTION
[0035] The materials, compounds, compositions, and methods described herein may be understood more readily by reference to the following detailed description of specific aspects of the disclosed subject matter and the Examples and Figures included therein.
[0036] Before the present materials, compounds, compositions, and methods are disclosed and described, it is to be understood that the aspects described below are not limited to specific synthetic methods or specific reagents, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting.
[0037] Also, throughout this specification, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which the disclosed matter pertains. The references disclosed are also individually and specifically incorporated by reference herein for the material contained in them that is discussed in the sentence in which the reference is relied upon.
[0038] Disclosed herein are compounds and methods for treating cancers. The compound is represented by X-Y-Z (Formula I) or a pharmaceutically acceptable salt thereof; wherein X is a destabilization amino acid residue Y is a linker, and Z is a ligand that binds a receptor tyrosine kinase. This compound and/or a pharmaceutical composition comprising this compound is useful for treating various cancers by degrading a receptor tyrosine kinase in the cancer cell.
[0039] Terms used throughout this application are to be construed with ordinary and typical meaning to those of ordinary skill in the art. However, Applicant desires that the following terms be given the particular definition as defined below.
Terminology
[0040] As used in the specification and claims, the singular form "a," "an," and "the" include plural references unless the context clearly dictates otherwise. For example, the term "an agonist" includes a plurality of agonist, including mixtures thereof.
[0041] Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the disclosure are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements. Furthermore, when numerical ranges of varying scope are set forth herein, it is contemplated that any combination of these values inclusive of the recited values may be used. Further, ranges can be expressed herein as from“about” one particular value, and/or to“about” another particular value. When such a range is expressed, another aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent“about,” it will be understood that the particular value forms another aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. Unless stated otherwise, the term“about” means within 5% (e.g., within 2% or 1%) of the particular value modified by the term“about.”
[0042]“Administration” to a subject includes any route of introducing or delivering to a subject an agent. Administration can be carried out by any suitable route, including oral, topical, intravenous, subcutaneous, transcutaneous, transdermal, intramuscular, intra-joint, parenteral, intra-arteriole, intradermal, intraventricular, intracranial, intraperitoneal, intralesional, intranasal, rectal, vaginal, by inhalation or via an implanted reservoir, and the like. Administration includes self
administration and the administration by another.
[0043] As used herein, the term "comprising" is intended to mean that the compositions and methods include the recited elements, but not excluding others. "Consisting essentially of" when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination. Thus, a composition consisting essentially of the elements as defined herein would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives, and the like. "Consisting of" shall mean excluding more than trace elements of other ingredients and substantial method steps for administering the compositions of this invention. Embodiments defined by each of these transition terms are within the scope of this invention.
[0044]“Dysregulation” refers herein refers to an abnormal level of expression or activity of a protein or gene. This can include, for example, less levels or activities than in normal healthy humans. This can also include, for example, increased levels or activities than in normal healthy humans. In some embodiments, disclosed herein comprises a cancer results from a dysregulation of a receptor tyrosine kinase.
[0045] "Inhibit," "inhibiting," and "inhibition" mean to decrease an activity, response, condition, disease, or other biological parameter. This can include but is not limited to the complete ablation of the activity, response, condition, or disease. This may also include, for example, a 10% reduction in the activity, response, condition, or disease as compared to the native or control level. Thus, the reduction can be a 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels.
[0046] "Ligand" refers herein to a molecule that acts on a target in a desirable manner. Examples of actions on a target in a desirable manner include, but are not limited to binding of the target, catalytically changing the target, reacting with the target in a way which modifies/alters the target or the functional activity of the target, covalently attaching to the target as in a suicide inhibitor, facilitating the reaction between the target and another molecule. In most, but not all, instances this desirable manner is binding to the target. The ligand can be an organic compound or other chemical. The ligand can be a compound, which is obtainable from or produced by any suitable source, whether natural or artificial. The ligand can be an amino acid molecule, a polypeptide, a peptide or a chemical derivative thereof, or a combination thereof. The ligand can also be a polynucleotide molecule - which can be a sense or an anti-sense molecule. The ligand can even be an antibody. In some embodiments, the“ligand” refers to any ligand that binds to or be bound by a receptor tyrosine kinase. In some embodiments, the“ligand” refers to any ligand that binds to or be bound by a non-receptor tyrosine kinase
[0047] "Tyrosine kinases” herein refer to a family of enzymes that catalyze the phosphorylation of select tyrosine residues in the target proteins by using ATP.
[0048]“Receptor tyrosine kinases” or“RTKs” are used interchangeably herein to refer to a family of membrane receptors that phosphorylate tyrosine residues. Receptor tyrosine kinases possess an extracellular ligand binding domain, a transmembrane domain and an intracellular catalytic domain. The extracellular domains bind cytokines, growth factors or other ligands and are generally comprised of one or more identifiable structural motifs, including cysteine-rich regions, fibronectin III- like domains, immunoglobulin- like domains, EGF-like domains, cadherin-like domains, kringle-like domains, Factor VIITlike domains, glycine-rich regions, leucine -rich regions, acidic regions and discoidin-like domains. Activation of the intracellular kinase domain is achieved by ligand binding to the extracellular domain, which induces dimerization of the receptors. A receptor activated in this way is able to autophosphorylate tyrosine residues outside the catalytic domain, facilitating stabilization of the active receptor conformation. The phosphorylated residues also serve as binding sites for proteins which will then transduce signals within the cell. Some RTKs are the high- affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer. Many play significant roles in development or cell division. In some embodiments, the RTK is estrogen-related receptor a. In some embodiments, the RTK is epidermal growth factor receptor.“Non-receptor tyrosine kinases” refer to a second subgroup of tyrosine kinases that are cytosolic enzymes. Non-receptor tyrosine kinases relay intracellular signals originating from extracellular receptor.
[0049] The terms“prevent,”“preventing,”“prevention,” and grammatical variations thereof as used herein, refer to a method of partially or completely delaying or precluding the onset or recurrence of a disease and/or one or more of its attendant symptoms or barring a subject from acquiring or reacquiring a disease or reducing a subject’s risk of acquiring or reacquiring a disease or one or more of its attendant symptoms.
[0050] The term“subject” refers to a human in need of treatment for any purpose, and more preferably a human in need of treatment to treat a disease or disorder, such as a cancer. The term “subject” can also refer to non-human animals, such as dogs, cats, horses, cows, pigs, sheep and non-human primates, among others.
[0051] "Pharmaceutically acceptable" component can refer to a component that is not biologically or otherwise undesirable, i.e., the component may be incorporated into a pharmaceutical formulation of the invention and administered to a subject as described herein without causing significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the formulation in which it is contained. When used in reference to administration to a human, the term generally implies the component has met the required standards of toxicological and manufacturing testing or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration.
[0052] "Pharmaceutically acceptable carrier" (sometimes referred to as a“carrier”) means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non-toxic, and includes a carrier that is acceptable for veterinary and/or human
pharmaceutical or therapeutic use. The terms "carrier" or "pharmaceutically acceptable carrier" can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil/water or water/oil emulsion) and/or various types of wetting agents.
[0053] As used herein, the term“carrier” encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in
pharmaceutical formulations. The choice of a carrier for use in a composition will depend upon the intended route of administration for the composition. The preparation of pharmaceutically acceptable carriers and formulations containing these materials is described in, e.g., Remington's Pharmaceutical Sciences, 21st Edition, ed. University of the Sciences in Philadelphia, Lippincott, Williams & Wilkins, Philadelphia, PA, 2005. Examples of physiologically acceptable carriers include saline, glycerol, DMSO, buffers such as phosphate buffers, citrate buffer, and buffers with other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™ (ICI, Inc.; Bridgewater, New Jersey), polyethylene glycol (PEG), and PLURONICS™ (BASF; Florham Park, NJ). To provide for the administration of such dosages for the desired therapeutic treatment, compositions disclosed herein can advantageously comprise between about 0.1% and 99% by weight of the total of one or more of the subject compounds based on the weight of the total composition including carrier or diluent.
[0054]“Pharmaceutically acceptable salt” as used herein refers to any salt that is pharmaceutically acceptable and has the desired pharmacological properties. Such salts are, for example, inorganic or organic base addition salts, or inorganic or organic acid addition salts. Each possibility represents a separate embodiment.
[0055] As used herein, the terms“treating” or“treatment” of a subject includes the administration of a drug to a subject with the purpose of curing, healing, alleviating, relieving, altering, remedying, ameliorating, improving, stabilizing or affecting a disease or disorder, or a symptom of a disease or disorder. The terms“treating” and“treatment” can also refer to reduction in severity and/or frequency of symptoms, elimination of symptoms and/or underlying cause, and improvement or remediation of damage.
[0056]“Therapeutic agent” refers to any composition that has a beneficial biological effect.
Beneficial biological effects include both therapeutic effects, e.g., treatment of a disorder or other undesirable physiological condition, and prophylactic effects, e.g., prevention of a disorder or other undesirable physiological condition (e.g., a cancer). The terms also encompass pharmaceutically acceptable, pharmacologically active derivatives of beneficial agents specifically mentioned herein, including, but not limited to, salts, esters, amides, proagents, active metabolites, isomers, fragments, analogs, and the like. When the terms“therapeutic agent” is used, then, or when a particular agent is specifically identified, it is to be understood that the term includes the agent per se as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, proagents, conjugates, active metabolites, isomers, fragments, analogs, etc.
[0057]“Therapeutically effective amount” or“therapeutically effective dose” of a composition (e.g. a composition comprising a compound of Formula I) refers to an amount that is effective to achieve a desired therapeutic result. In some embodiment, a desired therapeutic result is the treatment of a cancer. In some embodiment, a desired therapeutic result is the treatment of chronic myeloid leukemia, acute lymphocytic leukemia, breast cancer, or lung cancer. Therapeutically effective amounts of a given therapeutic agent will typically vary with respect to factors such as the type and severity of the disorder or disease being treated and the age, gender, and weight of the subject. The term can also refer to an amount of a therapeutic agent, or a rate of delivery of a therapeutic agent (e.g., amount over time), effective to facilitate a desired therapeutic effect, such as coughing relief. The precise desired therapeutic effect will vary according to the condition to be treated, the tolerance of the subject, the agent and/or agent formulation to be administered (e.g., the potency of the therapeutic agent, the concentration of agent in the formulation, and the like), and a variety of other factors that are appreciated by those of ordinary skill in the art. In some instances, a desired biological or medical response is achieved following administration of multiple dosages of the composition to the subject over a period of days, weeks, or years.
[0058] Reference will now be made in detail to specific aspects of the disclosed materials, compounds, compositions, articles, and methods, examples of which are illustrated in the accompanying Examples and Figures.
Compounds [0059] In some aspects, disclosed herein is a compound of Formula I:
X-Y-Z
Formula I wherein:
X is a destabilization amino acid residue;
Y is a linker; and
Z is a ligand that binds a tyrosine kinase;
or a pharmaceutically acceptable salt thereof.
[0060]“Destabilization amino acid residue” is used herein to refer to an amino acid reside that can destabilize a protein if the amino acid residue is at the N-terminus, following the“N-end rule”. The “N-end rule” states that the stability of a protein or a peptide is largely determined by the presence of“destabilizing” or“stabilizing” N-terminal amino acids. In some embodiments, the
destabilization amino acid residue can be, for example, Arg, His, Lys, Leu, lie, Phe, Trp, Tyr, Cys, Asn, Asp, Glu, or Gin. In some embodiments, the destabilization amino acid residue is Arg. In some embodiments, the destabilization amino acid residue is His. This single, destabilizing residue (e.g. Arg or His) at the N-terminus of a protein targets the substrate to a ubiquitin ligase termed Ubrl for rapid degradation via the N-end rule pathway.
[0061] In some embodiments, Z is a ligand binds a receptor tyrosine kinase. In some embodiments, Z is a ligand binds a non-receptor tyrosine kinase. The receptor tyrosine kinase described herein can be of any receptor tyrosine kinase. In some embodiments, the receptor tyrosine kinase comprises estrogen-related receptor a or epidermal growth factor receptor. In some embodiments, the receptor tyrosine kinase is estrogen-related receptor a. In some embodiments, the receptor tyrosine kinase is epidermal growth factor receptor. Thus, in some embodiments, the compound disclosed herein comprises a ligand binds estrogen-related receptor a. In some embodiments, the disclosed herein comprises a ligand binds epidermal growth factor receptor. In some embodiments, the non-receptor tyrosine kinase is Abelson tyrosine-protein kinase (ABL). Accordingly, in some embodiments, the compound disclosed herein comprises a ligand that binds ABL. In some embodiments, the compound disclosed herein comprises a ligand that binds BCR- ABL fusion protein.
[0062]“Estrogen-related receptor a” or“ERR a” refers to estrogen-related receptor a polypeptide and, in humans, is encoded by the ESRRA gene. In some embodiments, the estrogen-related receptor a polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 3471, Entrez Gene: 2101, Ensembl: ENSG00000173153, OMIM: 601998, and UniProtKB: PI 1474. In some embodiments, the estrogen-related receptor a is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NO: l. In some embodiments, the estrogen-related receptor a is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:l. In some embodiments, the estrogen-related receptor a is a polypeptide comprising SEQ ID NO: 1.
[0063]“Epidermal growth factor receptor” or“EGFR” refers to epidermal growth factor receptor polypeptide and, in humans, is encoded by the EGFR gene. In some embodiments, the epidermal growth factor receptor polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 3236, Entrez Gene: 1956, Ensembl: ENSG00000146648, OMIM: 131550, or UniProtKB: P00533. In some embodiments, the epidermal growth factor is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NO: 2. In some embodiments, the epidermal growth factor is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:2. In some embodiments, the epidermal growth factor is a polypeptide comprising SEQ ID NO:2.
[0064]“Abelson tyrosine-protein kinase” or“ABL” refers to Abelson tyrosine-protein kinase polypeptide and, in humans, is encoded by the ABL1 gene. In some embodiments, the Abelson tyrosine-protein kinase polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 76, Entrez Gene: 25, Ensembl: ENSG00000097007,
OMIM: 189980, UniProtKB: P00519. In some embodiments, the Abelson tyrosine-protein kinase is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NOG. In some embodiments, the Abelson tyrosine-protein kinase is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NOG. In some embodiments, the Abelson tyrosine-protein kinase is a polypeptide comprising SEQ ID NOG.
[0065]“Breakpoint cluster region protein” or“BCR” refers to breakpoint cluster region protein and, in humans, is encoded by the BCR gene. In some embodiments, the breakpoint cluster region polypeptide or polynucleotide is that identified in one or more publicly available databases as follows: HGNC: 1014, Entrez Gene: 613, Ensembl: ENSG00000186716, OMIM: 151410, UniProtKB: PI 1274. In some embodiments, the breakpoint cluster region protein is a polypeptide comprising an amino acid sequence which is at least 80% identical to SEQ ID NO:4. In some embodiments, the breakpoint cluster region is a polypeptide comprising an amino acid sequence which is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:4. In some embodiments, the breakpoint cluster region is a polypeptide comprising SEQ ID
NO:4.
[0066] In some embodiments, the ligand comprises an anti-cancer drug. The anti-cancer drug can be any anti-cancer drug targeting a receptor tyrosine kinase (e.g., estrogen-related receptor a or epidermal growth factor receptor). The anti-cancer drug includes, but not limited to, gefitinib, imatinib, erlotinib, sunitinib, lapatinib, trastuzumab, cetuximab, cevacizumab, nilotinib, sorafenib, crizotinib, panitumumab, or a thiazolidinedione derivative. In some embodiments, the ligand is gefitinib. In some embodiments, the ligand is imatinib. In some embodiments, the anti-cancer drug can be any anti-cancer drug targeting a non-receptor tyrosine kinase (e.g., ABL). In some embodiments, the anti-cancer drug targets BCR- ABL fusion protein. In some embodiments, the ligand is dasatinib.
[0067] The structure of gefitinib is shown below:
Figure imgf000018_0001
[0068] The structure of dasatinib is shown below:
Figure imgf000018_0002
[0069] The structure of imatinib is shown below:
Figure imgf000018_0003
[0070] In some embodiments, the ligand is a thiazolidinedione derivative. The functional group of a thiazolidinedione is shown below:
Figure imgf000019_0001
[0071] In some embodiments, the ligand is selected from the group consisting of pioglitazone, rosiglitazone, lobeglitazone, ciglitazone, garglitazone, englitazone, netoglitazone, rivoglitazone, troglitazone, and balaglitazone.
[0072] It should be understood that the thiazolidinedione derivative can be any thiazolidinedione derivative binding a receptor tyrosine kinase, including, for example, estrogen related receptor-a.
[0073] In some embodiments, the thiazolidinedione derivative can be any one of the those disclosed in Application W02008109727A1, which is incorporated by reference herein in its entirety for its teaching of thiazolidinedione derivatives. In some embodiments, the
thiazolidinedione derivative has a formula (I)
Figure imgf000019_0003
(I), wherein
Rl is halo, optionally substituted Ci-4alkyl, optionally substituted Ci-4alkoxy, or hydroxyl; R2 is selected from halo substituted Ci-3alkyl, cyano, halo, -C(0)NH2, and -C(0)0-Ci-4alkyl, or alternatively R2 is linked together to R3 to form an aryl fused to the phenyl ring to which R2 and R3 are shown attached; R3 is H, or alternatively R3 is linked together to R2 to form an aryl fused to the phenyl ring to which R3 and R2 are shown attached; R4 is halo, cyano, -CºCH, halo substituted Ci-3alkyl, -C(0)0-Ci-4alkyl, -C(0)NH2, or -S(02)-Ci-4alkyl; and X is S or O; or an optical isomer, enantiomer, diastereomer, cis-trans isomer, racemate, prodrug or pharmaceutically acceptable salt thereof.
[0074] In some embodiments, the structure of the thiazolidine derivative is shown blow:
Figure imgf000019_0002
[0075] In some embodiments, the linker (Y) comprises one or more covalently connected structural unit of A (e.g.,-Ai...An-), wherein Ai is covalently linked to an X moiety and An is covalently linked to a Z moiety, wherein the n is an integer greater than or equal to 0. In some embodiments, the n is greater than or equal to 1.
[0076] In some embodiments, e. g., wherein n is greater than 2, An is a group which is connected to a Z moiety, and Ai and An are connected via structural units of A (number of such structural units of A: n-2). In some embodiments, the q is 1, the structure of the linker group X is -Ai-, and Ai is a group which is connected to an X moiety and a Z moiety. In some embodiments, n is an integer from 1 to 100, 1 to 90, 1 to 80, 1 to 70, 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to 20, or 1 to 10.
[0077] In some embodiments, Y can be absent (i.e., X moiety can be bound directly Z moiety). In other embodiments, Y is present. When present, the linking group can be any suitable group or moiety which is at minimum bivalent, and connects the heterocyclic rings in the nucleophile. The linking group can be composed of any assembly of atoms, including oligomeric and polymeric chains. In some cases, the total number of atoms in the linking group can be from 3 to 200 atoms (e.g., from 3 to 150 atoms, from 3 to 100 atoms, from 3 and 50 atoms, from 3 to 25 atoms, from 3 to 15 atoms, or from 3 to 10 atoms). In some embodiments, the linking group can be, for example, an alkyl, alkoxy, alkylaryl, alkylheteroaryl, alkylcycloalkyl, alkylheterocycloalkyl, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, dialkylamino, alkylcarbonyl, alkoxycarbonyl,
alkylaminocarbonyl, dialkylaminocarbonyl, or polyamino group.
[0078] In some embodiments, the linking group can comprise one of the groups above joined to each of the heterocyclic rings by a functional group. Examples of suitable functional groups include, for example, secondary amides (-CONH-), tertiary amides (-CONR-), secondary carbamates (-OCONH-; -NHCOO-), tertiary carbamates (-OCONR-; -NRCOO-), ureas (- NHCONH-; -NRCONH-; -NHCONR-, or -NRCONR-), carbinols ( -CHOH-, -CROH-), ethers (- 0-), and esters (-COO-, -CH2O2C-, CHRO2C-), wherein R is an alkyl group, an aryl group, or a heterocyclic group. For example, in some embodiments, the linking group can comprise an alkyl group (e.g., a C1-C12 alkyl group, a Ci-Cs alkyl group, or a C1-C6 alkyl group) bound to each heterocyclic ring via an ester (-COO-, -CH2O2C-, CHRO2C-), a secondary amide (-CONH-), or a tertiary amide (-CONR-), wherein R is an alkyl group, an aryl group, or a heterocyclic group. The linking group can also comprise a polyalkoxyl group (e.g., -polyethyloxy, polypropyloxy). In certain embodiments, Y can be chosen from one of the following:
Figure imgf000020_0001
Figure imgf000021_0001
where each m is, independent of any other, an integer from 1 to 12.
[0079] In some embodiments, R1 can be absent. In other embodiments, R1 can be present. When present, R1 can comprise a halogen, hydroxy, amino, cyano, azido, hydrazone, alkyl, alkenyl, alkynyl, alkoxy, aryl, heteroaryl, alkylaryl, alkylheteroaryl, cycloalkyl alky ley cloalkyl, heterocycloalkyl, alkylheterocycloalkyl, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, dialkylamino, alkylcarbonyl, alkoxycarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, peptidyl, polyamino, or polyalkyleneoxy group.
[0080] In some embodiments, R1 can comprise a cationic group. In certain embodiments, the cationic group can comprise a cationic polyamino group (e.g., a polyethyleneimine segment). In other embodiments, the cationic group can comprise a cationic peptidyl group. In other embodiments, the cationic group can comprise a moiety (e.g., an alkyl group or an alkylaryl group) substituted with a cationic substituent, such as an ammonium group (e.g., a tetraalkylammonium group, an aryltrialkylammonium group, a diaryldialkylammonium group, or a
triarylalkylammonium group) or a pyridinium group.
[0081] In some embodiments, R1 can comprise a hydrophobic group. For example, in certain embodiments, R1 can comprise an aryl group or an alkylaryl group. In some embodiments, R1 can comprise a hydrophilic group. For example, in certain embodiments, R1 can comprise a hydrophilic polyalkyleneoxy group (e.g., a polyethylene oxide segment).
[0082] In some embodiments, R1 can comprise a reactive functional group, such as an olefin, acetylene, alcohol, phenol, ether, oxide, halide, aldehyde, ketone, carboxylic acid, ester, amide, cyanate, isocyanate, thiocyanate, isothiocyanate, amine, hydrazine, hydrazone, hydrazide, diazo, diazonium, nitro, nitrile, mercaptan, sulfide, disulfide, sulfoxide, sulfone, sulfonic acid, sulfinic acid, acetal, ketal, anhydride, sulfate, sulfenic acid isonitrile, amidine, imide, imidate, nitrone, hydroxylamine, oxime, hydroxamic acid, thiohydroxamic acid, allene, ortho ester, sulfite, enamine, ynamine, urea, pseudourea, semicarbazide, carbodiimide, carbamate, imine, azide, azo group, azoxy group, nitroso group, N-hydroxysuccinimide ester, or maleimides. For example, in certain embodiments, R1 can comprise an alkynyl group or an azido group. In other embodiments, R1 can comprise a hydrazone group.
[0083] In some embodiments, the compound has a molecular weight no more than 2000 daltons, 1900 daltons, 1800 daltons, 1700 daltons, 1600 daltons, 1500 daltons, 1400 daltons, 1300 daltons, 1200 daltons, 1100 daltons, 1000 daltons, 990 daltons, 980 daltons, 970 daltons, 960 daltons, 950 daltons, 940 daltons, 930 daltons, 930 daltons, 920 daltons, 910 daltons, 900 daltons, 890 daltons, 880 daltons, 870 daltons, 860 daltons, 850 daltons, 840 daltons, 830 daltons, 820 daltons, 810 daltons, 800 daltons, 790 daltons, 780 daltons, 770 daltons, 760 daltons, 750 daltons, 740 daltons, 730 daltons, 720 daltons, 710 daltons, 700 daltons, 690 daltons, 680 daltons, 670 daltons, 660 daltons, 650 daltons, 640 daltons, 630 daltons, 620 daltons, 610 daltons, 600 daltons, 590 daltons, 580 daltons, 570 daltons, 560 daltons, 550 daltons, 540 daltons, 530 daltons, 520 daltons, 510 daltons, 500 daltons, 490 daltons, 480 daltons, 470 daltons, 460 daltons, 450 daltons, 440 daltons, 430 daltons, 420 daltons, 410 daltons, 400 daltons, 390 dalton, 380 daltons, 370 daltons, 360 daltons, 350 daltons, 340 daltons, 330 daltons, 320 daltons, 310 daltons, 300 daltons, 290 daltons, 280 daltons, 270 daltons, 260 daltons, 250 daltons, 240 daltons, 230 daltons, 220 daltons, 210 daltons, or 200 daltons. In some embodiments, the compound has a molecular weight no more than 1000 daltons. In some embodiments, the compound has a molecular weight no more than 900 daltons.
[0084] In some embodiments, the compound is selected from the group consisting of:
Figure imgf000022_0001
Figure imgf000023_0001
[0085] In some aspects, disclosed herein is a pharmaceutical composition comprising the compound any preceding aspect, and a pharmaceutically acceptable carrier.
Methods of cancer therapy
[0086] Disclosed here in is a method for treating a cancer in a subject in need thereof, comprising: administering a therapeutically effective amount of a compound of Formula I:
X-Y-Z
Formula I wherein:
X is a destabilization amino acid residue;
Y is a linker; and
Z is a ligand that binds a tyrosine kinase;
or a pharmaceutically acceptable salt thereof.
[0087] In some embodiments, the cancer results from a dysregulation of the tyrosine kinase.
“Dysregulation” refers herein refers to an abnormal level of expression or activity of a protein or gene. This can include, for example, less levels or activities than in normal healthy humans. This can also include, for example, increased levels or activities than in normal healthy humans. In some embodiments, disclosed herein comprises a cancer results from a dysregulation of a receptor tyrosine kinase (e.g., estrogen-related receptor a or epidermal growth factor receptor) and/or a non receptor tyrosine kinase (e.g., ABL). Thus, the present invention encompasses a method for treating any cancer having a dysregulation of the receptor tyrosine kinase and/or a non-receptor tyrosine kinase. These cancer can be, for example, lymphoma, B cell lymphoma, T cell lymphoma, mycosis fungoides, Hodgkin’s Disease, myeloid leukemia, bladder cancer, brain cancer, nervous system cancer, head and neck cancer, squamous cell carcinoma of head and neck, lung cancers such as small cell lung cancer and non-small cell lung cancer, neuroblastoma/glioblastoma, ovarian cancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas of the mouth, throat, larynx, and lung, cervical cancer, cervical carcinoma, breast cancer, and epithelial cancer, renal cancer, genitourinary cancer, pulmonary cancer, esophageal carcinoma, head and neck carcinoma, large bowel cancer, hematopoietic cancers; testicular cancer; colon cancer, rectal cancer, prostatic cancer, or pancreatic cancer. In some embodiments, the cancer is chronic myeloid leukemia. In some embodiments, the cancer is acute lymphocytic leukemia. In some embodiments, the cancer is breast cancer. In some embodiments, the cancer is lung cancer. In some embodiments, the cancer is kidney cancer.
[0088] In some embodiments, the subject is a human. In some embodiments, the human has a cancer. In some embodiments, the human is suspected to have a cancer.
[0089] Dosing frequency for the compound, includes, but is not limited to, at least about once every 12 months, once every 11 months, one every 10 months, once every 9 months, once every 8 months, once every 7 months, once every 6 months, once every 5 months once every 4 months, once every once every 3 months, once every 12 weeks, once every 10 weeks, once every 8 weeks, once every 7 weeks, once every 6 weeks, once every 5 weeks, once every 4 weeks, once every 3 weeks, once every 2 weeks, or weekly. In some embodiments, the dosing frequency for the compound can be, for example, about once every 10 days, once every 9 days, once every 8 days, once every 7 days, once every 6 days, once every 5 days, once every 4 days, once every 3 days, once every 2 days, once every day, two times a day, three times a day, four times a day, five times a day, or six times a day. In some embodiments, the interval between each administration is less than about a week, such as less than about any of 6, 5, 4, 3, 2, or 1 day. In some embodiments, the interval between each administration can be more than a week, such as, more than two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, ten weeks, eleven weeks, twelve weeks, three months, four months, five months, or six months. In some
embodiments, the interval between each administration is constant. Administration can also be continuous and adjusted to maintaining a level of the compound within any desired and specified range.
EXAMPLES
[0090] Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. While the invention has been described with reference to particular embodiments and
implementations, it will be understood that various changes and additional variations may be made and equivalents may be substituted for elements thereof without departing from the scope of the invention or the inventive concept thereof. In addition, many modifications may be made to adapt a particular situation or device to the teachings of the invention without departing from the essential scope thereof. Such equivalents are intended to be encompassed by the following claims. It is intended that the invention not be limited to the particular implementations disclosed herein, but that the invention will include all implementations falling within the scope of the appended claims.
[0091] Cell cultures. The MCF-7 cell line (ATCC, Manassas, VA) was maintained at 37°C with 5% CO2 in DMEM with 2 mM L-glutamine that was modified to contain 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, and 1.5 g/1 sodium bicarbonate. It was also supplemented with 10% fetal bovine serum, 10 pg/ml bovine insulin, 100 units/pl penicillin/streptomycin. All drug treatment study was supplemented with 2% FBS. Functional assays including MTT, migration assays were done in 10% FBS in DMEM media
[0092] Cell proliferation assay. The (3-[4,5-dimethylthiazol-2-yl]-2, 5-diphenyl tetrazolium bromide) (MTT) method was used to measure living cells through mitochondrial dehydrogenase activity (Sigma Inc., Saint Louis, MO). Cells were plated in a 96-well, 5000 cells per 100 Dl/ well. After 24 h, the cells were treated with PROTACs in fresh media. At the indicated time point, the media was removed and dimethyl sulfoxide was added as MTT solubilization solution. Absorbance was measured at 550 nm.
[0093] Western blot analysis. Cells were lysed in RIPA buffer (Sigma Inc.) with the addition of protease inhibitors tablet and phosphatase inhibitors cocktail (Sigma Inc.). Lysates were resolved by SDS- polyacrylamide gels, transferred onto nitrocellulose membranes, and then probed with antibodies as indicated. Antibodies against ERRa, E-Cadherin, N-Cadherin, Snail, and GAPDH were obtained from Cell Signaling (Danvers, MA). Fibronectin antibody was obtained from Sigma Aldrich.
[0094] Wound healing assay. Cells were allowed to grow to near confluence in six well dishes. A uniform scratch was then made down the center of the plate using a 200 microliter micropipette tip, followed by washing twice with PBS. The same marked field of the scratch wound was photographed using an Olympus light microscope (4x objective) at the indicated time points. The width of the scratch wound was measured at three different areas with Image J software.
[0095] Migration assay. MCF-7 cells (lxlO4) were seeded on an 8 mM pore size Thin-cert for 24 well plates (Greiner Bio-One) in serum free media. PROTAC compounds were added to the bottom chamber as chemoattractant. After 48 h, cells on the top of the membrane were removed with a cotton swab. The migrated cells at the bottom side were washed with PBS, fixed with 70% ethanol and stained using 0.1% Crystal violet to visualize the migrated cells. Migrated cells attached to the lower side of the membrane were enumerated using a light microscope at lOx magnification.
Example 1. PROTAC Molecules and the Biological Effects Thereof
[0096] A short binding motif to a potent ubiquitin ligase can greatly improve the utility of the PROTAC approach. The shortest degradation motif is single amino acid, a destabilizing residue (e.g., Arg, His, Lys, Leu, lie) at the N-terminus of a protein that targets the substrate to a ubiquitin ligase termed Ubrl for rapid degradation via N-end rule pathway, the first ubiquitin dependent degradation pathway identified.
[0097] Ubrl is constitutive active and broadly expressed, making it ideally suited for this strategy. Adaptor molecules were synthesized starting with Arg and fused to a variety of cancer drugs. For example, Arg was appended to imatinib, a moiety specific for BCR-ABL protein. By linking BCR- ABL to Ubrl, the synthetic molecule can markedly reduce BCR-ABL level, which is key to chronic myeloid leukemia (CML) and acute lymphocytic leukemia (ALL). Improvements over existing strategies were achieved including: i) a small ubiquitin ligase-binding motif (i.e. Arg), markedly reducing the size of an adaptor, which increases cell permeability and efficacy; ii) the employment of Ubrl, a broadly expressed, potent ubiquitin ligase; iii) the Arg residue can be easily replaced with others (e.g. Lys, His) that changes the degradation speed due to different affinity for Ubrl, allowing optimal modulation of protein stability.
[0098] Adaptor molecules were synthesized starting with Arg or His and fused to a ligand for estrogen-related receptora (ERRa) (Fig. 1 A), a nuclear receptor that is a major regulator of several critical metabolic pathways and also is a prognostic marker of breast cancer. ERRa inhibition has been shown to reduce the proliferation of breast tumor cells in vitro and in vivo. It was found that both compounds reduced endogenous ERRa level in the MCF-7 metastatic breast cancer cell line (Fig. IB and Fig. 1C). To assess whether ERRa decrease was due to protein turnover, the cells were treated with cycloheximide to block protein synthesis and collected the samples at various time points for western blotting analysis. Both of these compounds triggered ERRa degradation (Fig. ID).
[0099] In addition, more fusion molecules were synthesized (Figs. 2A-2D) derived from gefitinib to target EGFR in lung cancer cells (H1299, H1975, HCC827, H3255), imatinib and dasatinib to target BCR-ABL protein in leukemia cells (e.g., K562, EM3, NAML1, KCL22, LAMA84, SUP- B15), and thiazolidinedione-based ligand for ERRa in breast cancer cells (e.g., MCF7, MDA-MB- 231). The drugs (e.g., gefitinib, imatinib, dasatinib) have been previously analyzed and are effective in target inhibition albeit resistance often occurs later developed. In addition to these novel Arg- based molecules, more molecules using chemical mimics of Arg are generated. The capacity of these fusion molecules (e.g., Arg-gefitinib chimera) in triggering rapid degradation of their targets (e.g., EGFR, BCR-ABL, ERRa) are tested in mammalian cells as well as their physiological effects (e.g., cell proliferation, receptor signaling, apoptosis) in relevant cancer cells. In addition, their efficacy in mouse xenograft models, and ultimately in affected leukemia patients are evaluated.
[00100] The chemical structure of an example of adaptor molecules synthesized starting with Arg or His and fused to a ligand for estrogen-related receptor a (ERRa) was shown (Fig. 3A), as introduced above (Figs. 1A-1D). It was shown herein that both compounds Arg-TERRa and His- TERRa reduced endogenous ERRa level in the MCF-7 metastatic breast cancer cell line (Fig. 3B).
To assess whether ERRa decrease was due to protein turnover, the cells were treated with cycloheximide to block protein synthesis and collected the samples at various time points for western blotting analysis. Both Arg-TERRa and His-TERRa triggered ERRa degradation (Fig. 3C).
[00101] Whether PROTAC-induced ERRa degradation is mediated by the proteasome was then evaluated. Arg-TERRa or His-TERRa-triggered ERRa turnover was compromised upon the treatment of the proteasome inhibitor MG132 (Fig. 4A and Fig. 4B), indicating the involvement of the proteasome in ERRa turnover. To ascertain that ERRa is degraded by the N-end rule pathway, dipeptides starting with a destabilizing residue (e.g., Arg, His) were utilized to block the degradation of N-end rule substrates through their competition for the ubiquitin ligase Ubrl. It was found that the PROTAC-exposed ERRa level was increased upon the addition of the dipeptide Arg- Ala or His-Ala, but not the control peptide Ala- Ala bearing a stabilizing residue (Fig. 4C and Fig. 4D).
[00102] The biological effects of the PROTAC molecules were examined in MCF-7 cells. Both compounds led to decreased proliferation of MCF-7 cells (Fig. 5A). As cell migration is key to tumorigenesis, evaluation was performed regarding whether the compounds affect cell motility by the scratch wound healing method and the ThinCert cell migration assay. Both Arg-TERRa and His- TERRa reduced MCF-7 cancer cell migration and wound repair (Fig. 5B and Fig. 5C).
Furthermore, assessment was performed to monitor the expression of several markers of epithelial- mesenchymal transition (EMT) that is crucial for cancer cell migration and invasion. PROTACs- induced ERRa destruction led to increased expression of E-cadherin and reduced expression of N- cadherin, SNAIL and Fibroectin (Fig. 5D), indicating EMT is repressed upon ERRa depletion. Combined, these results show that Arg-TERRa and His-TERRa can effectively modulate ERRa and be explored for anticancer purpose.The present disclosure shows that the N-end rule based PROTACs efficiently trigger target destruction and inhibit the proliferation of breast cancer cells.
[00103] The advantage of this approach lies in the use of the simplest degradation signal - single amino acid, which can be any one of the thirteen destabilizing residues in the N-end rule pathway that in turn can lead to different degradation speed. The PROTAC method presented here overcomes limitations of existing approaches with significantly smaller molecular size of E3 targeting moiety, leading to higher permeability and better efficacy, and a modulatable potent degradation activity, allowing better control and broader application. Furthermore, the N-end rule degradation pathway is universally present and constitutively active, making it ideally suited for the PROTAC approach. This modular design expands the repertoire of limited ubiquitin pathways currently available for PROTACs and can be easily adapted for broad use in targeted protein degradation.
Example 2. Peptides, Compounds, Experimental Procedures for Synthesis and Spectroscopic data
[00104] Details of Arg-TERRa and His-TERRa syntheses are described in Figs. 7-10 and Figs. 11-13, respectively. Dipeptides Arg-Ala and His-Ala were purchased from Bachem Americas (Torrance, CA). MG132 is a proteasome inhibitor obtained from Calbiochem (Gibbstown, NJ). Cyclohexamide was purchased from Sigma-Aldrich (Saint Louis, MO).
[00105] Unless otherwise mentioned, all reactions were carried out under a nitrogen atmosphere with dry solvents under anhydrous conditions. All the chemicals were purchased commercially and used without further purification. Anhydrous THF was distilled from sodium- benzophenone, and dichloroethane and dichloromethane were distilled from calcium hydride.
Yields refer to chromatographically. Reagents were purchased at the highest commercial quality and used without further purification, unless otherwise stated.
[00106] Reactions were monitored by Thin Layer Chromatography on plates (GF254) supplied by Yantai Chemicals (China) using UV light as visualizing agent and an ethanolic solution of phosphomolybdic acid and cerium sulfate, and heat as developing agents. If not specially mentioned, flash column chromatography uses silica gel (200-300 mesh) supplied by Tsingtao Haiyang Chemicals (China).
[00107] NMR spectra were recorded on Briiker Advance 500 (1H 500 MHz, 13C 125 MHz) and Briiker Advance 400 (1H 400 MHz, 13C 100 MHz) and are calibrated using residual undeuterated solvent (CDC13 at 7.26 ppm 1H NMR, 77.16 ppm 13C NMR; pyridine-d5 at 8.70 ppm 1H NMR, 149.6 ppm 13C NMR). The following abbreviations were used to explain the multiplicities: s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet, br = broad.
[00108] Mass spectrometric data were obtained using Briiker Apex IV FTMS using ESI (electrospray ionization) and Waters GCT (GC-MS) using El (electron impact ionization).
[00109] It will be appreciated that variants of the above-disclosed and other features and functions, or alternatives thereof, may be combined into many other different systems or applications. Various presently unforeseen or unanticipated alternatives, modifications, variations, or improvements therein may be subsequently made by those skilled in the art which are also intended to be encompassed by the following claims.
SEQUENCES
SEQ ID NO: l
MSSQVVGIEP LYIKAEPASP DSPKGSSETE TEPPVALAPG PAPTRCLPGH KEEEDGEGAG PGEQGGGKLV LSSLPKRLCL VCGDVASGYH YGVASCEACK AFFKRTIQGS IEYSCPASNE CEITKRRRKA CQACRFTKCL RVGMLKEGVR LDRVRGGRQK YKRRPEVDPL PFPGPFPAGP LAV AGGPRKT AAPVNALVSH LLVVEPEKLY AMPDPAGPDG HLPAVATLCD LFDREIVVTI SWAKSIPGFS SLSLSDQMSV LQSVWMEVLV LGVAQRSLPL QDELAFAEDL VLDEEGARAA GLGELGAALL QLVRRLQALR LEREEYVLLK ALALANSDSV HIEDAEAVEQ LREALHEALL EYEAGRAGPG GGAERRRAGR LLLTLPLLRQ TAGKVLAHFY GVKLEGKVPM HKLFLEMLEA MMD
SEQ ID NO:2
MRPS GT AG A ALL ALL A ALCPAS RALEEKKVCQGTS NKLTQLGTFEDHFLS LQRMFNNCE V
VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVL
SNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQN
HLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTG
PRESDCLVCRKFRDEATCKDTCPPLMLYNPTTY QMDVNPEGKY SFGATCVKKCPRNYVV
TDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKN
CTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEI
IRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQK
TKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPRE
FVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVW
KYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFM
RRRHIVRKRTLRRLLQERELVEPLTPS GE APN Q ALLRILKETEFKKIKVLGS G AFGT V YKGL
WIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQL
MPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQH
VKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTF
GS KP YDGIPAS EIS S ILEKGERLPQPPICTID V YMIM VKCWMID ADSRPKFRELIIEFS KM ARD
PQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLL
SSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPK RPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQ KGSHQISLDNPD Y QQDFFPKE AKPN GIFKGS TAEN AE YLR V APQS S EFIG A
SEQ ID NOG
MLEICLKL V GCKS KKGLS S S S SC YLEE ALQRPV ASDFEPQGLSE A ARWN S KENLL AGPSEN
DPNLFV AL YDFV AS GDNTLS ITKGEKLRVLG YNHN GEWCE AQTKN GQGW VPSN YITP VN
SLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDG
KLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDI
TMKHKLGGGQ Y GE V YEG VWKKY SLT V A VKTLKEDTMEVEEFLKE A A VMKEIKHPNL V Q
LLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIH
RDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSD
VWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWN
PSDRPSFAEIHQAFETMFQESSISDEVEKELGKQGVRGAVSTLLQAPELPTKTRTSRRAAEH
RDTTD VPEMPHS KGQGESDPLDHEPA VSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFS A
LIKKKKKTAPTPPKRSSSFREMDGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSN
GAGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHG
AKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRL
VKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPHKEEAGKGSALGTPAA
AEPVTPTSKAGSGAPGGTSKGPAEESRVRRHKHSSESPGRDKGKLSRLKPAPPPPPAASAG
KAGGKPS QS PS QE A AGE A VLG AKTKATS L VD A VNSD A AKPS QPGEGLKKPVLPATPKPQS
AKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQPPERIASGAITKGVVL
DSTEALCLAISRNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAINKLENNL
RELQICPAT AGS GPA ATQDFS KLLS S VKEIS DI V QR
SEQ ID NO:4
MVDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQELERCKASIRRLEQEVNQERFRMIYLQT LLAKEKKSYDRQRWGFRRAAQAPDGASEPRASASRPQPAPADGADPPPAEEPEARPDGEG SPGKARPGTARRPGAAASGERDDRGPPASVAALRSNFERIRKGHGQPGADAEKPFYVNVE FHHERGLVKVNDKEVSDRISSLGSQAMQMERKKSQHGAGSSVGDASRPPYRGRSSESSCG VDGD YED AELNPRFLKDNLID ANGGSRPPWPPLEY QPY QSIYV GGMMEGEGKGPLLRS QS TSEQEKRLTWPRRSYSPRSFEDCGGGYTPDCSSNENLTSSEEDFSSGQSSRVSPSPTTYRMF RDKSRSPSQNSQQSFDSSSPPTPQCHKRHRHCPVVVSEATIVGVRKTGQIWPNDGEGAFHG D ADGSFGTPPG Y GC A ADRAEEQRRHQDGLP YIDDS PS S SPHLS S KGRGSRD AL V S GALES T KASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTSQQIETIF
FKVPELYEIHKEFYDGLFPRVQQWSHQQRVGDLFQKLASQLGVYRAFVDNYGVAMEMAE
KCCQ AN AQFAEIS ENLR ARS NKD AKDPTTKN S LETLLYKPVDR VTRS TLVLHDLLKHTPAS
HPDHPLLQDALRISQNFLSSINEEITPRRQSMTVKKGEHRQLLKDSFMVELVEGARKLRHV
FLFTDLLLCTKLKKQSGGKTQQYDCKWYIPLTDLSFQMVDELEAVPNIPLVPDEELDALKI
KISQIKNDIQREKRANKGSKATERLKKKLSEQESLLLLMSPSMAFRVHSRNGKSYTFLISSD
YERAEWRENIREQQKKCFRSFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFL
NVIVHSATGFKQSSNLYCTLEVDSFGYFVNKAKTRVYRDTAEPNWNEEFEIELEGSQTLRI
LC YEKC YNKTKIPKEDGES TDRLMGKGQ V QLDPQ ALQDRD W QRT VI AMN GIE VKLS VKF
NSREFSLKRMPS RKQTG VFG VKIA V VTKRERS KVPYIVRQC VEEIERRGMEEV GI YR V S G V
ATDIQALKAAFDVNNKDVSVMMSEMDVNAIAGTLKLYFRELPEPLFrDEFYPNFAEGIALS
DPVAKESCMLNLLLSLPEANLLTFLFLLDHLKRVAEKEAVNKMSLHNLATVFGPTLLRPSE
KESKLPANPSQPITMTDSWSLEVMSQVQVLLYFLQLEAIPAPDSKRQSILFSTEV

Claims

What is claimed is:
A compound of Formula I:
X-Y-Z
Formula I wherein:
X is a destabilization amino acid residue;
Y is a linker; and
Z is a ligand that binds a tyrosine kinase;
or a pharmaceutically acceptable salt thereof.
2. The compound of claim 1, wherein the destabilization amino acid residue is selected from the group consisting of Arg, His, Lys, Leu, lie, Phe, Trp, Tyr, Cys, Asn, Asp, Glu, and Gin.
3. The compound of claim 2, wherein the destabilization amino acid residue is Arg or His.
4. The compound of any one of claims 1 to 3, wherein the tyrosine kinase is a receptor tyrosine kinase or a non-receptor tyrosine kinase.
5. The compound of claim 4, wherein the receptor tyrosine kinase comprises estrogen-related receptor a or epidermal growth factor receptor.
6. The compound of any one of claims 1 to 5, wherein the ligand comprises an anti-cancer drug.
7. The compound of claim 6, wherein the anti-cancer drug comprises gefitinib, dasatinib,
imatinib, or a thiazolidinedione derivative.
8. The compound of any one of claims 1 to 7, wherein the compound has a molecular weight no more than 1000 daltons.
9. The compound of any one of claims 1 to 8, wherein the compound is selected from the group consisting of
Figure imgf000033_0001
Figure imgf000034_0001
10. A pharmaceutical composition comprising the compound of any one of claims 1 to 9 and a pharmaceutically acceptable carrier.
11. A method for treating a cancer in a subject in need thereof, comprising: administering a
therapeutically effective amount of the pharmaceutical composition of claim 10.
12. The method of claim 11, wherein the cancer results from a dysregulation of the tyrosine kinase.
13. The method of claim 11 or 12, wherein the cancer comprises chronic myeloid leukemia, acute lymphocytic leukemia, breast cancer, or lung cancer.
14. The method of any one of claims 11 to 13, wherein the subject is a human.
15. A method for treating a cancer in a subject in need thereof, comprising: administering a
therapeutically effective amount of a compound of Formula I: X-Y-Z
Formula I wherein:
X is a destabilization amino acid residue;
Y is a linker; and
Z is a ligand that binds a tyrosine kinase;
or a pharmaceutically acceptable salt thereof.
16. The method of claim 15, wherein the destabilization amino acid residue is selected from the group consisting of Arg, His, Lys, Leu, lie, Phe, Trp, Tyr, Cys, Asn, Asp, Glu, and Gin.
17. The method of claim 16, wherein the destabilization amino acid residue is Arg or His.
18. The method of any one of claims 15 to 17, wherein the tyrosine kinase is a receptor tyrosine kinase or a non-receptor tyrosine kinase.
19. The method of claim 18, wherein the receptor tyrosine kinase comprises estrogen-related receptor a or epidermal growth factor receptor.
20. The method of any one of claims 15 to 19, wherein the ligand comprises an anti-cancer drug.
21. The method of claim 20, wherein the anti-cancer drug comprises gefitinib, dasatinib, imatinib, crizotinib, lapatinib, or a thiazolidinedione derivative.
22. The method of any one of claims 15 to 21, wherein the compound has a molecular weight no more than 1000 daltons.
23. The method of any one of claims 15 to 22, wherein the compound is selected from the group consisting of
Figure imgf000035_0001
Figure imgf000036_0001
24. The method of any one of claims 15 to 23, wherein the cancer results from a dysregulation of the tyrosine kinase.
25. The method of any one of claims 15 to 24, wherein the cancer comprises chronic myeloid leukemia, acute lymphocytic leukemia, breast cancer, or lung cancer.
26. The method of any one of claims 15 to 25, wherein the subject is a human.
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US20130190340A1 (en) * 2010-06-30 2013-07-25 Brandeis University Small-Molecule-Targeted Protein Degradation
WO2013106646A2 (en) * 2012-01-12 2013-07-18 Yale University Compounds and methods for the inhibition of vcb e3 ubiquitin ligase
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