WO2020117988A1 - Cdk9 inhibitors and polymorphs thereof for use as agents for treatment of cancer - Google Patents

Cdk9 inhibitors and polymorphs thereof for use as agents for treatment of cancer Download PDF

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Publication number
WO2020117988A1
WO2020117988A1 PCT/US2019/064549 US2019064549W WO2020117988A1 WO 2020117988 A1 WO2020117988 A1 WO 2020117988A1 US 2019064549 W US2019064549 W US 2019064549W WO 2020117988 A1 WO2020117988 A1 WO 2020117988A1
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WIPO (PCT)
Prior art keywords
compound
cancer
pharmaceutical composition
acid
tautomer
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Application number
PCT/US2019/064549
Other languages
French (fr)
Inventor
Adam Siddiqui-Jain
Paul Flynn
Yuji Fujiwara
Shuji Masumoto
Hiroaki Tanaka
Hirotaka Kurebayashi
Takahiko Hashizuka
Yuka ARIKAWA
Original Assignee
Tolero Pharmaceuticals, Inc.
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Publication date
Application filed by Tolero Pharmaceuticals, Inc. filed Critical Tolero Pharmaceuticals, Inc.
Priority to JP2021531721A priority Critical patent/JP2022511029A/en
Priority to CN201980080099.1A priority patent/CN113490499A/en
Priority to KR1020217020451A priority patent/KR20210099066A/en
Priority to AU2019391097A priority patent/AU2019391097A1/en
Priority to MX2021006544A priority patent/MX2021006544A/en
Priority to EP19892691.7A priority patent/EP3890749A4/en
Priority to CA3119807A priority patent/CA3119807A1/en
Publication of WO2020117988A1 publication Critical patent/WO2020117988A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
    • C07F9/02—Phosphorus compounds
    • C07F9/06—Phosphorus compounds without P—C bonds
    • C07F9/08—Esters of oxyacids of phosphorus
    • C07F9/09—Esters of phosphoric acids
    • C07F9/095—Compounds containing the structure P(=O)-O-acyl, P(=O)-O-heteroatom, P(=O)-O-CN
    • C07F9/096—Compounds containing the structure P(=O)-O-C(=X)- (X = O, S, Se)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/66—Phosphorus compounds
    • A61K31/675—Phosphorus compounds having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/0012—Galenical forms characterised by the site of application
    • A61K9/0053—Mouth and digestive tract, i.e. intraoral and peroral administration
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/20—Pills, tablets, discs, rods
    • A61K9/2004—Excipients; Inactive ingredients
    • A61K9/2013—Organic compounds, e.g. phospholipids, fats
    • A61K9/2018—Sugars, or sugar alcohols, e.g. lactose, mannitol; Derivatives thereof, e.g. polysorbates
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/20—Pills, tablets, discs, rods
    • A61K9/2004—Excipients; Inactive ingredients
    • A61K9/2022—Organic macromolecular compounds
    • A61K9/205—Polysaccharides, e.g. alginate, gums; Cyclodextrin
    • A61K9/2054—Cellulose; Cellulose derivatives, e.g. hydroxypropyl methylcellulose
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/20—Pills, tablets, discs, rods
    • A61K9/2004—Excipients; Inactive ingredients
    • A61K9/2022—Organic macromolecular compounds
    • A61K9/205—Polysaccharides, e.g. alginate, gums; Cyclodextrin
    • A61K9/2059—Starch, including chemically or physically modified derivatives; Amylose; Amylopectin; Dextrin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/48—Preparations in capsules, e.g. of gelatin, of chocolate
    • A61K9/4841—Filling excipients; Inactive ingredients
    • A61K9/4858—Organic compounds
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/48—Preparations in capsules, e.g. of gelatin, of chocolate
    • A61K9/4841—Filling excipients; Inactive ingredients
    • A61K9/4866—Organic macromolecular compounds
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
    • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
    • C07F9/02—Phosphorus compounds
    • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
    • C07F9/6558—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system
    • C07F9/65586—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom containing at least two different or differently substituted hetero rings neither condensed among themselves nor condensed with a common carbocyclic ring or ring system at least one of the hetero rings does not contain nitrogen as ring hetero atom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2300/00—Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
    • C07B2200/00—Indexing scheme relating to specific properties of organic compounds
    • C07B2200/13—Crystalline forms, e.g. polymorphs

Definitions

  • Alvocidib is a potent cyclin-dependent kinase (CDK) inhibitor with selectivity for CDKs 9, 1, 2, 4 and 7.
  • CDK cyclin-dependent kinase
  • Embodiments of the present invention are generally directed to CDK (e.g., CDK9) inhibitors and polymorphs thereof as well as pharmaceutical compositions comprising the same, for use as therapeutic or prophylactic agents, for example, for treatment of cancer (e.g., hematological cancer) and other conditions.
  • CDK e.g., CDK9
  • pharmaceutical compositions comprising the same, for use as therapeutic or prophylactic agents, for example, for treatment of cancer (e.g., hematological cancer) and other conditions.
  • cancer e.g., hematological cancer
  • Some embodiments provide a crystalline form of a compound having the structure (I):
  • aspects of the present disclosure are directed to a polymorph of a compound having the structure (I), or a tautomer or zwitterionic form thereof.
  • the polymorph has an X-ray powder diffraction pattern comprising the following: D space ( ⁇ ): 18.3 ⁇ 0.09, 8.1 ⁇ 0.06, 6.4 ⁇ 0.08, 5.9 ⁇ 0.06, 4.4 ⁇ 0.05 expressed in terms of“D” spacing.
  • One embodiment provides a crystalline form of a compound of structure (I), or a tautomer or zwitterionic form thereof, having an x-ray powder diffraction pattern substantially in accordance with that depicted in FIG.1.
  • Yet another embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph is Form B as described herein.
  • Still another embodiment affords a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph is formed by a method comprising (a) contacting an amorphous compound of structure (I) with a lattice forming reagent; and (b) treating the product of step (a) with solvent having water content less than about 0.05% v/v and removing the solvent, thereby forming the polymorph.
  • One embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • One embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof having an endotherm peak value at about 256°C– 268°C as determined by differential scanning calorimetry.
  • compositions comprising a compound having structure (I) (e.g., a polymorph or crystalline form of a compound having structure (I)), or a tautomer or zwitterionic form thereof, and a pharmaceutically acceptable carrier or excipient are also provided in various other embodiments.
  • a pharmaceutical composition comprising from about 0.5 weight percent to about 11.25 weight percent of a compound having the structure (I), or a tautomer or zwitterionic form thereof; and from about 85 weight percent to about 99.5 weight percent of a pharmaceutically acceptable carrier or excipient.
  • One embodiment provides a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer or zwitterionic form thereof; about 97.4 weight percent of anhydrous lactose; about 1 weight percent colloidal silicon dioxide; and about 1 weight percent magnesium stearate.
  • Another embodiment provides a pharmaceutical composition comprising about 11 weight percent of a compound having the structure (I), or a tautomer or zwitterionic form thereof; about 87 weight percent of anhydrous lactose; about 1 weight percent colloidal silicon dioxide; and about 1 weight percent magnesium stearate.
  • Yet another embodiment provides a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer or zwitterionic form thereof; and from about 98 weight percent to about 99.5 weight percent of cornstarch.
  • Another embodiment provides a pharmaceutical composition comprising about 11 weight percent of a compound of the structure (I), or a tautomer or zwitterionic form thereof; and about 88 weight percent of cornstarch.
  • inventions provide methods including a method for treatment of a disease associated with overexpression of a cyclin-dependent kinase (CDK), such as cancer (e.g., a hematologic cancer), in a mammal in need thereof, for example, by administering to the mammal a therapeutically effective amount of a crystalline form or a polymorph of a compound having structure (I), or a tautomer or zwitterionic form thereof.
  • CDK cyclin-dependent kinase
  • the present disclosure provides a method for preparing a polymorph or crystalline form of the compound of structure (I).
  • One embodiment provides a method for preparing crystalline Form B of a compound having structure (II):
  • Another embodiment provides a method for preparing crystalline Form B of the compound having structure (II), the method comprising contacting a compound having structure (V):
  • Yet another embodiment provides a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting a compound having the following structure (IV):
  • di-tert-butylhalophosphonate e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate
  • di-tert-butylhalophosphonate e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate
  • an acid having a pKa value of greater than about 1 e.g., an acid having at least one pK a value that is less than about 5 and a pK a value of greater than about 1
  • Another embodiment is a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; contacting the compound having structure (V), or a tautomer or salt thereof, with an acid having a pKa value of less than about 1, thereby forming a salt of a compound having structure (I); contacting the salt of a compound having structure (I) with a base, thereby forming amorphous compound having structure (I); and contacting the amorphous form of the compound having structure (I), in an organic solvent, with an acid having a pKa value of greater than about 1 (e
  • the present disclosure also provides methods for preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof.
  • the method comprises contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert-butylchlorophosphonate, di-tert- butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof, with an acid, thereby preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof.
  • di-tert-butylhalophosphonate e.g., di-tert-butylchlorophosphonate, di-tert- butylbromophosphonate
  • FIG.1 illustrates an x-ray diffractogram obtained from XRPD analysis for polymorph Form B.
  • FIG.2 shows a stability profile in the form of a TG-FTIR thermogram and a DSC spectrum for the amorphous form of structure (I) (i.e., Form A).
  • FIG.3 illustrates a comparison of lattice forming reagents and the similarity of diffractogram patterns as determined by XRPD for polymorph Form B.
  • FIG.4 depicts the Oak Ridge Thermal Ellipsoid Plot (ORTEP) diagrams of single crystal structure obtained for polymorph Form B.
  • FIG.5 shows diffractograms from XRPD analysis of three samples of polymorph Form C.
  • FIG.6A-6B show TG-FTIR thermograms of polymorph Form C before (FIG.6A) and after drying (FIG.6B).
  • FIG.7 shows a comparison of 1 H NMR spectra acquired for forms A (amorphous), form B (polymorph) and form C.
  • FIG.8 shows the differential scanning calorimetry output of heat flow plotted as a function of temperature for polymorph form B.
  • FIG.9A is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and filler in the excipient compatibility study described in Example 13.
  • FIG.9B is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and lubricant in the excipient compatibility study described in Example 13.
  • FIG.9C is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and disintegrant in the excipient compatibility study described in Example 13.
  • FIG.9D is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and fluidizer/other excipient in the excipient compatibility study described in Example 13.
  • FIG.10A is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-01 of Example 14 stored at 5 °C.
  • FIG.10B is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-01 of Example 14 stored at 25 °C and 60% relative humidity (RH).
  • FIG.10C is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-01 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10D is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-02 of Example 14 stored at 5 °C.
  • FIG.10E is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-02 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10F is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-02 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10G is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-03 of Example 14 stored at 5 °C.
  • FIG.10H is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-03 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10I is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-03 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10J is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-04 of Example 14 stored at 5 °C.
  • FIG.10K is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-04 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10L is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-04 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10M is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-05 of Example 14 stored at 5 °C.
  • FIG.10N is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-05 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10O is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-05 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10P is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-06 of Example 14 stored at 5 °C.
  • FIG.10Q is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-06 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10R is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-06 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10S is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-08 of Example 14 stored at 5 °C.
  • FIG.10T is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-08 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10U is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-08 of Example 14 stored at 40 °C and 75% RH.
  • FIG.10V is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-09 of Example 14 stored at 5 °C.
  • FIG.10W is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-09 of Example 14 stored at 25 °C and 60% RH.
  • FIG.10X is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-09 of Example 14 stored at 40 °C and 75% RH.
  • FIG.11A is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 1 on day 1 following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • FIG.11B is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 1 on day 14 following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • FIG.11C is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 2 on day 1 following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • FIG.11D is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 2 on day 14 following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • FIG.11E is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in Cohort 5 on day 1 following daily oral BID dosing with 6 mg of Formulation No.401-01.
  • FIG.11F is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in Cohort 5 on day 14 following daily oral BID dosing with 6 mg of Formulation No.401-01.
  • FIG.11G is a graph of alvocidib (ng/mL) versus cohort, and shows the average Cmax of alvocidib on day 1 and day 14 following daily oral QD dosing with a 1- mg strength capsule containing Formulation No.401-01.
  • FIG.11H is a graph of alvocidib (ng*hr/mL) versus cohort, and shows the area under the curve (AUC) of alvocidib on day 1 (AUC0-8) and day 14 (AUC0-8 and AUC0-24) following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • FIG.11I is a graph of mean concentration of alvocidib (nM) versus time, and shows the mean concentration of alvocidib in plasma of Cohort 5 patients over a 24-hour period.
  • FIG.12 is a graph, and shows the completed cycles on the study described in Example 15 through Cohort 5.
  • Crystal refers to a homogeneous solid formed by a repeating, three-dimensional pattern of atoms, ions or molecules having fixed distances between constituent parts. The unit cell is the simplest repeating unit in this pattern. Notwithstanding the homogenous nature of an ideal crystal, a perfect crystal rarely, if ever, exists.“Crystalline,” as used herein, encompasses crystalline forms that include crystalline defects, for example, crystalline defects commonly formed by manipulating (e.g., preparing, purifying) the crystalline forms described herein. A person skilled in the art is capable of determining whether a sample of a compound is crystalline notwithstanding the presence of such defects.
  • Polymorph refers to a crystalline form of a compound characterized by a distinct arrangement of its molecules in a crystal lattice. Polymorphs can be characterized by analytical methods such as x-ray powder diffraction (XRPD), differential scanning calorimetry (DSC) and thermogravimetric analysis.
  • the crystalline forms and/or polymorphs described herein can be substantially pure.
  • “substantially pure,” used without further qualification means the indicated compound has a purity greater than 90 weight percent, for example, greater than 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 weight percent, and also including a purity equal to about 100 weight percent, based on the weight of the compound.
  • the remaining material comprises other form(s) of the compound, and/or reaction impurities and/or processing impurities arising from its preparation (e.g., alvocidib).
  • “Substantially pure” can also be qualified as in“substantially pure of other physical forms of the compound having structure (I), or a tautomer or zwitterionic form thereof” or“substantially pure of alvocidib.”
  • “substantially pure” means that the indicated compound contains less than 10%, preferably less than 5%, more preferably less than 3%, most preferably, less than 1% by weight of the indicated impurity (e.g., any other physical forms of an indicated crystalline form of a compound; alvocidib).
  • the term“alvocidib” means 2-(2-chlorophenyl)-5,7- dihydroxy-8-[(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]chromen-4-one, or a salt (e.g., a pharmaceutically acceptable salt) thereof (e.g., 2-(2-chlorophenyl)-5,7-dihydroxy-8- [(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]chromen-4-one hydrochloride).
  • An XRPD pattern or DSC thermogram that is“substantially in accordance” with one or more figures herein showing an XRPD pattern or diffractogram or DSC thermogram, respectively, is one that would be considered by one skilled in the art to represent the same single crystalline form of the compound having structure (I), or a tautomer or zwitterionic form thereof, as the sample of the compound having structure (I), or a tautomer or zwitterionic form thereof, that provided the pattern or
  • an XRPD pattern or DSC thermogram that is substantially in accordance may be identical to that of one of the figures or, more likely, may be somewhat different from one or more of the figures.
  • an XRPD pattern that is somewhat different from one or more of the figures may not necessarily show each of the lines of the diffraction pattern presented herein and/or may show a slight change in appearance or intensity of the lines or a shift in the position of the lines. These differences typically result from differences in the conditions involved in obtaining the data or differences in the purity of the sample used to obtain the data.
  • a person skilled in the art is capable of determining if a sample of a crystalline compound is of the same form as or a different form from a form disclosed herein by comparison of the XRPD pattern or DSC thermogram of the sample and the corresponding XRPD pattern or DSC thermogram disclosed herein.
  • the crystalline forms provided herein can also be identified on the basis of differential scanning calorimetry (DSC) and/or thermogravimetric analysis (TGA).
  • DSC is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample is measured as a function of temperature. DSC can be used to detect physical transformations, such as phase transitions, of a sample. For example.
  • DSC can be used to detect the temperature(s) at which a sample undergoes crystallization, melting or glass transition. It is to be understood that any temperature associated with DSC specified herein, with the exception of the DSC temperatures in the Figures or Examples, means the specified value ⁇ 5 °C or less. For example, when an embodiment or a claim specifies an endothermic peak at 264 °C, this is to be understood to mean 264 °C ⁇ 5 °C or less, that is a temperature of from 259 °C to 269 °C. In preferred embodiments, a DSC is the specified value ⁇ 3 °C or less, in more preferred embodiments, ⁇ 2 °C or less.
  • “Lattice forming reagent” or“salt former” refers to a chemical substance that is used in combination with another compound to facilitate the formation of a crystalline or polymorphic solid.
  • a lattice forming reagent facilitates the formation of polymorph Form B of the compound of structure (I).
  • Lattice forming reagents include acids, bases, sugars, peptides, and the like.
  • the lattice forming reagent is an acid (e.g., an acid having at least one pKa value that is less than about 5, such as about 4).
  • a lattice forming reagent may be an organic acid (e.g., maleic acid, acetic acid, fumaric acid, tartaric acid).
  • the acid is a diprotic acid.
  • the term“effective amount” or“therapeutically effective amount” refers to that amount of a compound (e.g., polymorph Form B of a compound of structure (I)) described herein that is sufficient to effect the intended application including disease treatment, as defined below.
  • the therapeutically effective amount may vary depending upon the intended treatment application (in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • the term also applies to a dose that will induce a particular response in target cells, e.g., reduction of platelet adhesion and/or cell migration.
  • the specific dose will vary depending on the particular compound chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
  • treatment refers to an approach for obtaining beneficial or desired results with respect to a disease, disorder or medical condition including a therapeutic benefit and/or a prophylactic benefit.
  • therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated.
  • a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder.
  • the compositions are administered to a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
  • A“therapeutic effect,” as that term is used herein, encompasses a
  • a prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
  • co-administration encompass administration of two or more agents to a subject, such as an animal, including humans, to treat a disease, disorder or condition described herein.
  • administration of the two or more agents is such that both agents and/or their metabolites are present in the subject at the same time.
  • Co-administration includes simultaneous administration in separate compositions, administration at different times in separate compositions, or
  • An“anti-cancer agent,”“anti-tumor agent” or“chemotherapeutic agent” refers to any agent useful in the treatment of a neoplastic condition.
  • One class of anti- cancer agents comprises chemotherapeutic agents.
  • “Chemotherapy” means the administration of one or more chemotherapeutic drugs and/or other agents to a cancer patient by various methods, including intravenous, oral, intramuscular, intraperitoneal, intravesical, subcutaneous, transdermal, buccal, or inhalation or in the form of a suppository.
  • Subject refers to an animal, such as a mammal, for example, a human.
  • the methods described herein can be useful in both human therapeutics and veterinary applications.
  • the subject is a mammal, and in some
  • the subject is human.
  • “Mammal” includes humans and both domestic animals such as laboratory animals and household pets (e.g., cats, dogs, swine, cattle, sheep, goats, horses, rabbits), and non-domestic animals, such as wildlife and the like. In some embodiments, the mammal is a human.
  • Radionuclides e.g., actinium and thorium radionuclides
  • LET low linear energy transfer
  • beta emitters conversion electron emitters
  • high-energy radiation including without limitation x-rays, gamma rays, and neutrons.
  • in vivo refers to an event that takes place in a subject’s body.
  • Embodiments of the invention disclosed herein are also meant to encompass crystallin forms and/or polymorphs of a compound of structure (I), or a tautomer or zwitterioninc form thereof, being isotopically-labelled by having one or more atoms replaced by an atom having a different atomic mass or mass number (i.e., an“isotopic form” of the crystalline forms and/or polymorphs of a compound of structure (I), or a tautomer or zwitterionic form thereof).
  • isotopes that can be incorporated into the disclosed crystalline forms and/or polymorphs, or a tautomer or zwitterionic form thereof, include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as 2 H, 3 H, 11 C, 13 C, 14 C, 13 N, 15 N, 15 O, 17 O, 18 O, 31 P, 32 P, 35 S, 18 F, 36 Cl, 123 I, and 125 I, respectively. These radiolabeled compounds could be useful to help determine or measure the effectiveness of the compounds, by
  • isotopically-labeled crystalline forms and/or polymorphs of compounds of structure (I), or a tautomer or zwitterionic form thereof, for example, those incorporating a radioactive isotope, are useful in drug and/or substrate tissue distribution studies.
  • the radioactive isotopes tritium (i.e., 3 H), and carbon-14 (i.e., 14 C) are particularly useful for this purpose in view of their ease of incorporation and ready means of detection.
  • Substitution with heavier isotopes such as deuterium may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage requirements, and hence are preferred in some circumstances.
  • positron emitting isotopes such as 11 C, 18 F, 15 O and 13 N
  • PET positron emission topography
  • Isotopically-labeled crystalline forms and/or polymorphs of compounds of structure (I), or a tautomer or zwitterionic form thereof can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described in the Examples as set out below using an appropriate isotopically-labeled reagent in place of the non-labeled reagent previously employed.
  • A“pharmaceutical composition” refers to a formulation of a compound of the disclosure and a medium generally accepted in the art for the delivery of the biologically active compound to mammals, e.g., humans.
  • a medium includes all pharmaceutically acceptable carriers, diluents or excipients therefor.
  • “Pharmaceutically acceptable carrier or excipient” includes without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye/colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier which has been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.
  • “Pharmaceutically acceptable salt” includes both acid and base addition salts.
  • “Pharmaceutically acceptable acid addition salt” refers to those salts which retain the biological effectiveness and properties of the free bases, which are not biologically or otherwise undesirable, and which are formed with inorganic acids such as, but are not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as, but not limited to, acetic acid, 2,2-dichloroacetic acid, adipic acid, alginic acid, ascorbic acid, aspartic acid, benzenesulfonic acid, benzoic acid, 4-acetamidobenzoic acid, camphoric acid, camphor-10-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecylsulfuric acid, ethane-1,2-d
  • naphthalene-1,5-disulfonic acid naphthalene-2-sulfonic acid, 1-hydroxy-2-naphthoic acid, nicotinic acid, oleic acid, orotic acid, oxalic acid, palmitic acid, pamoic acid, propionic acid, pyroglutamic acid, pyruvic acid, salicylic acid, 4-aminosalicylic acid, sebacic acid, stearic acid, succinic acid, tartaric acid, thiocyanic acid, p-toluenesulfonic acid, trifluoroacetic acid, undecylenic acid, and the like.
  • “Pharmaceutically acceptable base addition salt” refers to those salts which retain the biological effectiveness and properties of the free acids, which are not biologically or otherwise undesirable. These salts are prepared from addition of an inorganic base or an organic base to the free acid. Salts derived from inorganic bases include, but are not limited to, the sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Preferred inorganic salts are the ammonium, sodium, potassium, calcium, and magnesium salts.
  • Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as ammonia, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, diethanolamine, ethanolamine, deanol, 2-dimethylaminoethanol,
  • 2-diethylaminoethanol dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, benethamine, benzathine, ethylenediamine, glucosamine, methylglucamine, theobromine, triethanolamine, tromethamine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins and the like.
  • Particularly preferred organic bases are isopropylamine, diethylamine, ethanolamine,
  • A“tautomer” refers to a proton shift from one atom of a molecule to another atom of the same molecule. Embodiments thus include tautomers of the disclosed compounds, crystalline forms and polymorphs.
  • Zwitterionic form refers to a form of a compound, wherein at least one functional group has a positive electrical charge, at least one functional group has a negative electrical charge, and the net charge of the entire molecule is zero.
  • the phosphate group (-PO 3 H 2 ) of a compound having structure (I) may exist in an anionic form (e.g., -PO 3 H-), and the nitrogen atom of a compound having structure (I) may exist in the protonated (cationic) form.
  • the compound having structure (II) is a zwitterionic form of the compound having structure (I), for example.
  • Embodiments include zwitterions of the disclosed compounds, crystalline forms and polymorphs.
  • one embodiment provides a crystalline form of a compound having the following structure (I):
  • the crystalline form comprises Form B. In some embodiments, the crystalline form consists essentially of Form B. In some embodiments, the crystalline form consists of Form B. In some embodiments, the crystalline form (e.g., Form B) is substantially pure (e.g., of other physical forms of the compound having structure (I), or a tautomer or zwitterionic form thereof; of impurities; of alvocidib). In some embodiments, the crystalline form is of a compound having structure (II).
  • Form B has structure (II):
  • Form B is characterized by an XRPD pattern comprising peaks at the following 2-theta angles: 10.8 ⁇ 0.2°, 14.9 ⁇ 0.2° and 20.0 ⁇ 0.2°.
  • Form B is characterized by an XRPD pattern comprising peaks at the following 2-theta angles: 4.8 ⁇ 0.2°, 10.8 ⁇ 0.2°, 14.9 ⁇ 0.2° and 20.0 ⁇ 0.2°. In some embodiments, Form B is characterized by an XRPD pattern comprising peaks at the following 2-theta angles: 4.8 ⁇ 0.2°, 10.8 ⁇ 0.2°, 13.7 ⁇ 0.2°, 14.9 ⁇ 0.2° and 20.0 ⁇ 0.2°. In some embodiments, Form B has an XRPD pattern substantially in accordance with that depicted in FIG.1. In some embodiments, Form B is characterized by a DSC thermogram comprising an endothermic peak at about 264 °C. In some embodiments, Form B is characterized by a DSC thermogram substantially in accordance with that depicted in FIG.8.
  • One embodiment provides a polymorph of a compound having the following structure (I):
  • the polymorph having an X-ray powder diffraction pattern comprising the following:
  • the polymorph has an X-ray powder diffraction pattern comprising the following:
  • the polymorph has an X-ray powder diffraction pattern comprising the following:
  • One embodiment provides a polymorph of a compound of structure (I), or a tautomer or zwitterion thereof, wherein the polymorph is a crystalized form having a monoclinic space group P21 with lattice parameters of:
  • Another embodiment provides a polymorph of a compound of structure (I), or a tautomer or zwitterion thereof, wherein the polymorph is a crystalized form having a monoclinic space group P21 with lattice parameters of:
  • Yet another embodiment provides a polymorph of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has the X-ray diffraction pattern set forth in FIG.1 (or substantially similar). In some embodiments, the polymorph has the X-ray diffraction pattern substantially similar to Table 6. [00106] Another related embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph is Form B.
  • One embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof wherein the polymorph is formed by a method comprising: a) contacting an amorphous compound of structure (I) with a lattice forming reagent; and
  • step b) treating the product of step a) with solvent having water content less than about 0.05 % v/v and removing the solvent, thereby forming the polymorph.
  • the lattice forming reagent is maleic acid.
  • the solvent is ethanol or tetrahydrofuran.
  • the contacting further comprises suspending the amorphous compound of structure (I) in aqueous tetrahydrofuran.
  • Another embodiment affords a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days above a temperature of about 22°C.
  • the subsequent purity is at least 99.5% after being stored greater than about 7 days above a temperature of about 22°C. In some more specific embodiments, the subsequent purity is at least 99.5% after being stored greater than about 30 days above a temperature of about 20°C. In some embodiments, the initial purity and subsequent purity are as determined by HPLC.
  • the water content of the polymorph can have a significant effect on the purity and storage stability of the polymorph. That is, the polymorph can undergo a hydrolysis reaction that converts that phosphate moiety to a hydroxyl group. As such, an impurity may be present in the form of hydrolyzed structure (I) (i.e., alvocidib).
  • hydrolyzed structure (I) i.e., alvocidib
  • some embodiments provide a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days above a temperature at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • the subsequent purity is at least 99.5% after being stored for greater than about 7 days at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • the subsequent purity is at least 99.5% after being stored for greater than about 30 days at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • the initial purity and subsequent purity are as determined by HPLC.
  • Still other embodiments provide a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an endotherm peak value at about 256.0°C– 268.0 (i.e., 262.0°C ⁇ 6.0) as determined by differential scanning calorimetry.
  • the endotherm peak value is at a temperature ranging from 256°C to 268°C, from 257.0°C to 266.0°C or from 258.0°C to 265.0°C.
  • the endotherm peak value is at about 259.0°C– 265.0°C.
  • the polymorph comprises a zwitterionic form having the following structure (II):
  • the polymorph has water content less than 0.50 % as determined by Karl Fischer titration.
  • the polymorph has water content less than 0.45 %, less than 0.40 %, less than 0.35 %, less than 0.30 %, less than 0.25 %, less than 0.20 %, less than 0.15 %, or less than 0.10 % as determined by Karl Fischer titration.
  • reaction including an acid as lattice forming reagent may alternatively employ another suitable reagent such as a base, a sugar derivative, a peptide or other reagent.
  • One embodiment provides a method for preparing a polymorph, the method comprising: a) contacting an amorphous compound having the following structure (I):
  • step b) treating the product of step a) with solvent having water content less than about 0.05 % v/v; and removing the solvent, thereby forming the polymorph.
  • the lattice forming reagent is an acid.
  • the acid is an organic acid.
  • the acid is an acid having a pKa greater than 1.0.
  • the acid is a diprotic acid.
  • the acid is selected from the group consisting of maleic acid, fumaric acid, L-tartaric acid, hippuric acid, nicotinic acid, acetic acid, and combinations thereof.
  • the lattice forming reagent is maleic acid.
  • the contacting comprises adding the lattice forming reagent (e.g., maleic acid) in a 1:1 ⁇ 0.5 ratio (e.g., molar ratio) of the amorphous compound of structure (I) to maleic acid.
  • the ratio e.g., molar ratio
  • the ratio is 1:1 ⁇ 0.3, 1:1 ⁇ 0.2, or 1:1 ⁇ 0.1 compound of structure (I) to maleic acid.
  • the ratio e.g., molar ratio
  • the lattice forming reagent is not limited to acids and can be any other compound that can be mixed with a compound of structure (I) and forms polymorph Form B.
  • the lattice forming reagent is a sugar or a peptide.
  • the lattice forming reagent is D-xylose.
  • the lattice forming reagent is aspartame.
  • the removing step is performed to remove residual solvent and lattice forming reagent and afford a solid product as a free base. Accordingly, in some embodiments the removing may involve reduced pressure (e.g., below 1 atm), a flow of air or inter gas (e.g., N 2 ), increased temperature (e.g., above 25°C) or combinations thereof. In specific embodiments, the removing is at a pressure less than about 1 atm and a temperature greater than about 35°C. In some more specific embodiments, the pressure is less than about 0.9 atm, about 0.8 atm, about 0.7 atm, about 0.6 atm, or about 0.5 atm.
  • reduced pressure e.g., below 1 atm
  • a flow of air or inter gas e.g., N 2
  • increased temperature e.g., above 25°C
  • the removing is at a pressure less than about 1 atm and a temperature greater than about 35°C. In some more specific embodiments, the pressure is less than about 0.9 at
  • the temperature is above about 36 °C, about 37 °C, about 38 °C, about 39 °C, about 40 °C, about 42 °C, or about 45 °C. In some embodiments, the temperature is above the boiling point of residual solvent, e.g., about 100 °C.
  • the temperature and pressure values recited above include a range of ⁇ 5% of the recited value (i.e., about 45°C includes 45°C ⁇ 2.25°C).
  • the removing comprises filtering the solid product away from residual solvent and/or lattice forming reagent.
  • some embodiments of the methods recited above further comprise preparing a compound of structure (III):
  • the base is an amine base, (e.g., triethylamine, diisopropylethyl amine).
  • amine base is added in an organic solvent.
  • the method further comprises preparing the amorphous compound of structure (I):
  • the phosphoester cleaving compound is an organosilicon (e.g., trimethyl silyl bromide,“TMSBr”).
  • the basic solution comprises ammonium (e.g., ammonium bicarbonate).
  • the basic solution comprises acetonitrile.
  • the basic solution comprises aqueous acetonitrile.
  • the polymorph is a polymorph as described in the foregoing embodiments. Additionally, one embodiment provides a polymorph that is prepared according to any of the methods described herein. [00128] Thus, in any of the embodiments described herein involving polymorph conversion/formation (e.g., preparation of crystalline Form B of a compound having structure (II)), the polymorph conversion/formation step(s) comprise crystallizing compound having structure (I) (e.g., amorphous compound having structure (I)), or a tautomer or zwitterionic form thereof, from an acidic solution (e.g., having a pH of greater than about 1; having a pH of greater than about 1 to less than about 5, for example, from about 1 to about 4, from about 2 to about 5).
  • an acidic solution e.g., having a pH of greater than about 1; having a pH of greater than about 1 to less than about 5, for example, from about 1 to about 4, from about 2 to about 5.
  • the acidic solution comprises a lattice forming reagent (e.g., an acid, such as maleic acid; an acid having a pK a of greater than about 1; an acid having at least one pK a of less than about 5 and a pK a of greater than about 1, for example, at least one pK a of less than about 4 and a pKa of greater than about 1, at least one pKa of less than about 5 and a pK a of greater than about 2) and a solvent.
  • a lattice forming reagent e.g., an acid, such as maleic acid; an acid having a pK a of greater than about 1; an acid having at least one pK a of less than about 5 and a pK a of greater than about 1, for example, at least one pK a of less than about 4 and a pKa of greater than about 1, at least one pKa of less than about 5 and a pK
  • One embodiment is a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting amorphous compound having structure (I), or a tautomer or zwitterionic form thereof, with a lattice forming reagent (e.g., an acid, such as maleic acid; an acid having a pK a of greater than about 1; an acid having at least one pKa of less than about 5 and a pKa of greater than about 1, for example, an acid having at least one pKa of less than about 4 and a pKa of greater than about 1, an acid having at least one pK a of less than about 5 and a pK a of greater than about 2) in a solvent, thereby preparing the crystalline Form B of the compound having structure (II).
  • a lattice forming reagent e.g., an acid, such as maleic acid; an acid having a pK a of greater than about 1; an acid having
  • One embodiment is a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting a compound having structure (V):
  • the molar ratio of acid to compound having structure (V), or a tautomer, salt or zwitterionic form thereof is from about 0.1:1 to about 10:1 (e.g., from about 0.1:1 to about 5:1; from about 0.4:1 to about 1.1:1; about 0.5:1).
  • the lattice forming reagent is an acid.
  • the acid for preparing crystalline Form B has at least one pKa value that is less than about 5 (e.g., less than about 4) and/or a pK a value of greater than about 1 (e.g., greater than about 2).
  • the acid is an organic acid.
  • “organic acid” is an organic compound with acidic properties.
  • an organic acid contains at least one carboxyl group (-COOH).
  • Organic acids include, but are not limited to, maleic acid, acetic acid, citric acid and propionic acid.
  • the organic acid is maleic acid.
  • solvent refers to a liquid that serves as a medium for a chemical reaction or other procedure in which compounds are being manipulated (e.g., crystallization).
  • the solvent in the methods disclosed herein is an organic solvent or water, or a combination thereof.
  • organic solvents include polar, protic solvents (e.g., an alcohol such as methanol, ethanol, butanol), polar aprotic solvents (e.g., dimethylformamide, tetrahydrofuran, ethyl acetate, acetone, methyl ethyl ketone) or nonpolar solvents (e.g., diethyl ether).
  • the solvent comprises tetrahydrofuran.
  • the solvent is a mixture of methanol and acetone.
  • Also provided are methods for preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof e.g., a compound having structure (II)
  • the method comprises contacting a compound having the following structure (IV):
  • di-tert-butylhalophosphonate e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate
  • di-tert-butylhalophosphonate e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate
  • an acid e.g., maleic acid
  • the method further comprises contacting di-tert-butylphosphonate with carbon tetrahalide (e.g., carbon tetrachloride, carbon tetrabromide) to prepare the di-tert-butylhalophosphonate (e.g., di- tert-butylchlorophosphonate, di-tert-butylbromophosphonate, respectively).
  • the di-tert-butylhalophosphonate is prepared in situ with the compound having structure (IV), or a salt thereof, by contacting di-tert-butylphosphonate with carbon tetrahalide (e.g., carbon tetrachloride, carbon tetrabromide).
  • carbon tetrahalide e.g., carbon tetrachloride, carbon tetrabromide
  • the acid is hydrochloric acid or acetic acid, or a combination thereof.
  • Amine base refers to a compound that contains a nitrogen atom with a lone pair.“Amine base” includes primary, secondary and tertiary amine bases, as well as ammonia. Typically, the amine base is an organic amine base.
  • organic amine bases include, but are not limited to, diisopropylethylamine, tert-butylamine and triethylamine.
  • a salt e.g., a hydrochloride salt
  • the compound formed by contacting a compound having structure (V), or a tautomer or salt thereof, with an acid is a salt of a compound having structure (I).
  • the method further comprises contacting the salt of the compound having structure (I) with a base (e.g., ammonium bicarbonate), thereby forming the compound having structure (I), or a tautomer or zwitterionic form thereof.
  • a base e.g., ammonium bicarbonate
  • One embodiment is a method for preparing crystalline Form B of a compound having structure (II).
  • the method comprises contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di- tert-butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof, in an organic solvent, with an acid having a pK a value of greater than about 1 (e.g., an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1, for example, at least one pK a value that is less than about 4 and a pK a value of greater than about 1, at least one pK a value that
  • Another embodiment is a method for preparing crystalline Form B of a compound having structure (II), comprising contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof (e.g., in an organic solvent) with an acid having a pK a value of less than about 1, thereby forming a salt of a compound having structure (I); contacting the salt of a compound having structure (I) with a base, thereby forming amorphous compound having structure (I); and contacting the amorphous compound having structure (I) with an acid having a pK a value of
  • the functional groups of intermediate compounds may need to be protected by suitable protecting groups.
  • suitable protecting groups for hydroxy include trialkylsilyl or diarylalkylsilyl (for example, t- butyldimethylsilyl, t-butyldiphenylsilyl or trimethylsilyl), tetrahydropyranyl, benzyl, and the like.
  • Suitable protecting groups for amino, amidino and guanidino include t- butoxycarbonyl, benzyloxycarbonyl, and the like.
  • Suitable protecting groups for mercapto include -C(O)-R" (where R" is alkyl, aryl or arylalkyl), p-methoxybenzyl, trityl and the like.
  • Suitable protecting groups for carboxylic acid include alkyl, aryl or arylalkyl esters.
  • Protecting groups are optionally added or removed in accordance with standard techniques, which are known to one skilled in the art and described herein. The use of protecting groups is described in detail in Green, T.W. and P.G.M. Wutz, Protective Groups in Organic Synthesis (1999), 3rd Ed., Wiley.
  • the protecting group may also be a polymer resin such as a Wang resin, Rink resin or a 2-chlorotrityl-chloride resin.
  • Embodiments of the polymorph of a compound of structure (I) as shown can be prepared according to General Reaction Scheme 1.
  • Certain intermediates useful for preparation of the compound having structure (I), or a tautomer, salt or zwitterionic form thereof e.g., A-1, A-2, A-3, A-4, A-10, A-11
  • A-1 can be purchased from commercial sources or prepared according to methods familiar to one of ordinary skill in the art.
  • Reaction of A-1 with a strong Lewis acid e.g., boron tribromide affords A-2, which can then be
  • an activated protected phosphate reagent e.g., diethyl
  • the phosphorylated product (A-3) can then be deprotected under standard conditions (e.g., TMS-Br) and neutralized using suitable conditions (e.g., ammonium carbon ate in aqueous acetonitrile).
  • the resultant compound A-4 i.e., an amorphous solid or“Form A” which is then converted to the polymorph A-5 using an appropriate lattice forming reagent (e.g., maleic acid) and a suitable solvent system (e.g., THF and water at 19:1 v/v).
  • an appropriate lattice forming reagent e.g., maleic acid
  • a suitable solvent system e.g., THF and water at 19:1 v/v.
  • the lattice forming reagent is removed using a suitable, substantially anhydrous solvent (e.g., an alcohol such as ethanol) and dried to afford polymorph Form B.
  • General Reaction Scheme 2 describes another method for preparing Form A and Form B.
  • A-1 Reaction of A-1 with a strong Lewis acid (e.g., boron tribromide) affords A- 2, which can then be phosphorylated with an activated protected phosphate reagent (e.g., di-tert-butylhalophosphonate, such as di-tert-butylchlorophosphonate or di-tert- butylbromophosphonate) under basic conditions (e.g., using diisopropylethylamine as a base) in an appropriate solvent (e.g., dimethylformamide; DMF).
  • a strong Lewis acid e.g., boron tribromide
  • an activated protected phosphate reagent e.g., di-tert-butylhalophosphonate, such as di-tert-butylchlorophosphonate or di-tert- butylbromophosphonate
  • an appropriate solvent e.g., dimethylformamide; DMF
  • the di-tert-butylhalophosphonate can be prepared (e.g., in situ with A-2) by contacting di-tert- butylphosphonate with carbon tetrahalide (e.g., carbon tetrachloride, carbon
  • the phosphorylated product (A-10) can then be deprotected under acidic conditions (e.g., using hydrochloric and acetic acids).
  • acidic conditions e.g., using hydrochloric and acetic acids.
  • hydrochloride salt can then be converted to its free base and/or zwitterionic form, Form A (A-4), under neutralizing conditions (e.g., ammonium carbonate in aqueous acetonitrile).
  • the resultant compound A-4 can then be converted to Form B (A-5) using an appropriate lattice forming reagent (e.g., an acid, such as maleic acid, acetic acid, citric acid, propionic acid) and a suitable solvent (e.g., THF and water at 19:1 v/v, methanol, methanol and aceton at 1:1 v/v).
  • an appropriate lattice forming reagent e.g., an acid, such as maleic acid, acetic acid, citric acid, propionic acid
  • a suitable solvent e.g., THF and water at 19:1 v/v, methanol, methanol and aceton at 1:1 v/v.
  • the lattice forming reagent is removed from A-5 using a suitable, substantially anhydrous solvent (e.g., an alcohol such as ethanol), and resulting A-5 is dried to afford Form B.
  • A-10 can be deprotected and converted to Form B (A-5) under acidic conditions (e.g., maleic acid in methanol and acetone at 1:1 v/v) to afford Form B.
  • acidic conditions e.g., maleic acid in methanol and acetone at 1:1 v/v
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer e.g., a tautomer
  • the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is formulated into a pharmaceutical composition.
  • the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof can be the compound having structure (II), or any crystalline form or polymorph of a compound of structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof described herein, e.g., Form B.
  • a pharmaceutical composition, as used herein, refers to a mixture of the compound having structure (I) (e.g.
  • one embodiment provides a pharmaceutical composition
  • a pharmaceutical composition comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof, and a pharmaceutically acceptable carrier or excipient.
  • the pharmaceutical composition is formulated for oral administration.
  • Pharmaceutical compositions described herein are formulated by combining the active (e.g., crystalline form and/or polymorph of a compound having structure (I), or a tautomer or zwitterionic form thereof) with, e.g., pharmaceutically acceptable carriers or excipients.
  • the crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof is formulated in an oral dosage form that includes, by way of example only, tablets, powders, pills, dragees, capsules, liquids, gels, syrups, elixirs, slurries, suspensions and the like.
  • the pharmaceutical composition comprises an oral capsule.
  • the pharmaceutical composition comprises the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form), in a concentration ranging from about 0.5 weight percent to about 11.25 weight percent.
  • the pharmaceutical composition comprises the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form) in a concentration ranging from about 0.6 weight percent to about 11.05 weight percent.
  • the pharmaceutical composition comprises about 0.6 weight percent of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In other specific embodiments, the pharmaceutical composition comprises about 2.5 weight percent of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In still other specific embodiments, the pharmaceutical composition comprises about 11.0 weight percent of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form).
  • the pharmaceutical composition comprises about 1 milligram (mg) of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In other specific embodiments, the pharmaceutical composition comprises about 4 mg of the compound having structure (I), or a tautomer,
  • the pharmaceutical composition comprises about 16 mg of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form).
  • the excipient is anhydrous. In some embodiments, the excipient is anhydrous lactose or microcrystalline cellulose. In more specific embodiments, the excipient is anhydrous lactose. In some embodiments, the excipient is microcrystalline cellulose. In specific embodiments, the excipient is anhydrous microcrystalline cellulose.
  • the excipient is anhydrous lactose or cornstarch (e.g., cornstarch).
  • the pharmaceutical composition comprises the excipient in a concentration ranging from about 85 weight percent to about 98 weight percent. In more specific embodiments, the pharmaceutical composition comprises the excipient in a concentration ranging from about 87 weight percent to about 97.5 weight percent. In some embodiments, the pharmaceutical composition comprises about 87 weight percent of the excipient. In other words,
  • the pharmaceutical composition comprises about 95.5 weight percent of the excipient.
  • the pharmaceutical composition further comprises a glidant.
  • the glidant is colloidal silicon dioxide.
  • the pharmaceutical composition comprises about 1 weight percent of the glidant (e.g., colloidal silicon dioxide).
  • the pharmaceutical composition further comprises a lubricant.
  • the lubricant is magnesium stearate.
  • the pharmaceutical composition comprises about 1 weight percent of the lubricant (e.g., magnesium stearate).
  • Other examples of lubricants are described in Example 13 herein.
  • the pharmaceutical composition further comprises a disintegrant.
  • the disintegrant is partly
  • pregelatinized starch low-substituted hydroxyl propyl cellulose or carmellose calcium.
  • Other examples of disintegrants are described in Example 13 herein.
  • One embodiment is a pharmaceutical composition
  • a pharmaceutical composition comprising from about 0.5 weight percent to about 11.25 weight percent (e.g., from about 0.5 weight percent to about 1 weight percent, from about 10.5 weight percent to about 11.25 weight percent) of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), and from about 85 weight percent to about 99.5 weight percent (e.g., from about 95 weight percent to about 99.5 weight percent, from about 85 weight percent to about 90 weight percent, respectively) of a pharmaceutically acceptable carrier or excipient.
  • One embodiment is a pharmaceutical composition
  • a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), about 97.4 weight percent of anhydrous lactose, about 1 weight percent colloidal silicon dioxide, and about 1 weight percent magnesium stearate.
  • the pharmaceutical composition comprises about 1 mg of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)).
  • One embodiment is a pharmaceutical composition
  • a pharmaceutical composition comprising about 11 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), about 87 weight percent of anhydrous lactose, about 1 weight percent colloidal silicon dioxide, and about 1 weight percent magnesium stearate.
  • the pharmaceutical composition comprises about 16 mg of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)).
  • One embodiment is a pharmaceutical composition
  • a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), and from about 98 weight percent to about 99.5 weight percent of cornstarch.
  • the pharmaceutical composition further comprises about 1 weight percent magnesium stearate.
  • One embodiment is a pharmaceutical composition
  • a pharmaceutical composition comprising about 11 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), and about 88 weight percent of cornstarch.
  • the pharmaceutical composition further comprises about 1 weight percent magnesium stearate.
  • the pharmaceutical compositions are in the form of a capsule for oral administration.
  • a pharmaceutical composition described herein e.g., comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof
  • a rapid release formulation refers to a formulation that does not delay or prolong release of an active contained therein. Typically, rapid release formulations release at least 70% of the active contained therein within 1 hour. In some embodiments, a rapid release formulation releases at least 75% of an active contained therein (e.g., a compound having structure (I), or a tautomer,
  • Rapid release formulation is also referred to as“immediate release formulation.”
  • a pharmaceutical composition described herein e.g., comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof
  • extended release formulation refers to a formulation that releases an active contained therein in a controlled manner during an extended period of time, at a predetermined rate, duration, and location following administration.
  • a pharmaceutical composition described herein e.g., comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof
  • an intermediate release formulation refers to a formulation that delays or extends release of an active contained therein, or alters its site of release, but is not an extended release formulation, as that term is described herein.
  • the pharmaceutical composition may also be formulated for a route of administration other than oral.
  • routes of administration include intravenous, rectal, aerosol, parenteral, ophthalmic, pulmonary, transmucosal, transdermal, vaginal, otic, nasal, and topical administration.
  • parenteral delivery includes intramuscular, subcutaneous, intravenous, intramedullary injections, as well as intrathecal, direct intraventricular, intraperitoneal, intralymphatic, and intranasal injections.
  • a pharmaceutical composition described herein is administered in a local rather than systemic manner, for example, via injection of the pharmaceutical composition directly into an organ, often in a depot preparation or sustained release formulation.
  • long-acting formulations are administered by implantation (for example, subcutaneously or intramuscularly) or by intramuscular injection.
  • the pharmaceutical composition is delivered in the form of a targeted drug delivery system, for example, a liposome coated with organ-specific antibody. In such embodiments, the liposomes are targeted to and taken up selectively by the organ.
  • the pharmaceutical composition is provided in the form of a rapid release formulation, in the form of an extended release formulation, or in the form of an intermediate release formulation.
  • the pharmaceutical composition is administered topically.
  • the pharmaceutical composition is formulated for transmucosal administration.
  • transmucosal formulations include penetrants that are appropriate to the barrier to be permeated.
  • appropriate formulations include aqueous or non-aqueous solutions.
  • such solutions include physiologically compatible buffers and/or excipients.
  • compositions described herein are formulated for buccal or sublingual administration.
  • Formulations suitable for buccal or sublingual administration include, by way of example only, tablets, lozenges, or gels.
  • the pharmaceutical composition described herein is formulated for parental injection, including bolus injection or continuous infusion.
  • formulations for injection are presented in unit dosage form (e.g., in ampoules) or in multi-dose containers. Preservatives are, optionally, added to the injection formulations.
  • the pharmaceutical compositions are formulated in a form suitable for parenteral injection as sterile suspensions, solutions or emulsions in oily or aqueous vehicles.
  • Parenteral injection formulations optionally contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • suspensions are prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles for use in the
  • compositions described herein include, by way of example only, fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or
  • aqueous injection suspensions contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.
  • the suspension contains suitable stabilizers or agents which increase the solubility of the active to allow for the preparation of highly concentrated solutions.
  • suitable stabilizers or agents which increase the solubility of the active to allow for the preparation of highly concentrated solutions.
  • the active ingredient is in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
  • a suitable vehicle e.g., sterile pyrogen-free water
  • the pharmaceutical composition is administered in dosages. It is known in the art that due to intersubject variability in compound pharmacokinetics, individualization of dosing regimen is necessary for optimal therapy. Dosing for the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, may be found by routine experimentation in light of the instant disclosure.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof may be found by routine experimentation in light of the instant disclosure.
  • the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, according to certain embodiments, is effective over a wide dosage range.
  • dosages from 0.01 to 1000 mg, from 0.5 to 100 mg, from 1 to 50 mg per day, and from 5 to 40 mg per day are examples of dosages that are used in some embodiments.
  • An exemplary dosage is 10 to 30 mg per day. In various embodiments, the dosage is 3, 6, 9, 12, 16, 21, 28, 32, 42, or 50 mg per day.
  • the dosage ranges from about 1 mg to about 30 mg per day, e.g., about 1 mg, about 2 mg, about 4 mg, about 8 mg, about 12 mg, about 16 mg or about 22 mg per day.
  • the exact dosage will depend upon the route of administration, the form in which the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered, the subject to be treated, the body weight of the subject to be treated, and the preference and experience of the attending physician.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer e.g., a tautomer
  • a single dose of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, may also be used for treatment of an acute condition.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer e.g., a tautomer
  • dosing is about once, twice, three times, four times, five times, six times, or more than six times per day (e.g., twice per day). In other embodiments, dosing is about once a month, once every two weeks, once a week, or once every other day.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered about once per day to about 6 times per day.
  • the administration of the polymorph of a compound of structure (I) continues for less than about 7 days.
  • the administration continues for more than about 6, 10, 14, 28 days, two months, six months, or one year. In some cases, continuous dosing is achieved and maintained as long as necessary.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof may continue as long as necessary.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered for more than 1, 2, 3, 4, 5, 6, 7, 14, or 28 days.
  • the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered for less than 28, 14, 7, 6, 5, 4, 3, 2, or 1 day.
  • the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered chronically on an ongoing basis, e.g., for the treatment of chronic effects.
  • the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered once daily for the first 21 days out of a 28-day cycle.
  • the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered twice daily for the first 21 days out of a 28-day cycle.
  • a cycle may be repeated at least once, at least twice, at least three times, or at least four times.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered as a pharmaceutical composition in which the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form, is mixed with one or more other active ingredients, as in combination therapy.
  • a pharmaceutical combination comprising a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, and one or more additional therapeutic agents (e.g., chemotherapeutic agents).
  • additional therapeutic agents e.g., chemotherapeutic agents
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof has a water content less than 0.50%, as determined by Karl Fischer titration.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof has a water content less than 0.45%, less than 0.40%, less than 0.35%, less than 0.30%, less than 0.25%, less than 0.20%, less than 0.15%, or less than 0.10%, as determined by Karl Fischer titration.
  • a unit dose form comprising a pharmaceutical composition as described herein.
  • the unit dose form is formulated for oral administration.
  • the unit dose form is a capsule.
  • the unit dose form is a tablet.
  • dosage forms such as dragee cores and tablets, are provided with one or more suitable coatings.
  • suitable coatings such as dragee cores and tablets.
  • concentrated sugar solutions are used for coating the dosage form.
  • the sugar solutions optionally contain additional components, such as, by way of example only, gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs and/or pigments are also optionally added to the coatings for identification purposes.
  • dyestuffs and/or pigments are optionally utilized to characterize different combinations of active compound doses.
  • the unit dose form comprises the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, in a concentration ranging from about 0.5 weight percent to about 11.25 weight percent.
  • the unit dose form comprises the polymorph in a concentration ranging from about 0.6 weight percent to about 11.05 weight percent.
  • the unit dose form comprises about 0.6 weight percent of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In other specific embodiments, the unit dose form comprises about 2.5 weight percent of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
  • the unit dose form comprises about 11.0 weight percent of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • the unit dose form comprises about 1 milligram (mg) of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In other specific embodiments, the unit dose form comprises about 4 mg of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
  • the unit dose form comprises about 16 mg of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • the unit dose form comprises the excipient in a concentration ranging from about 85 weight percent to about 98 weight percent. In more specific embodiments, the unit dose form comprises the excipient in a concentration ranging from about 87 weight percent to about 97.5 weight percent. In some embodiments, the unit dose form comprises about 87 weight percent of the excipient. In other embodiments, the unit dose form comprises about 95.5 weight percent of the excipient.
  • the excipient is anhydrous. In some embodiments, the excipient is anhydrous lactose or microcrystalline cellulose. In more specific embodiments, the excipient is anhydrous lactose. In some embodiments, the excipient is microcrystalline cellulose. In specific embodiments, the excipient is anhydrous microcrystalline cellulose.
  • the excipient is anhydrous lactose or cornstarch.
  • the unit dose form further comprises a glidant.
  • the glidant is colloidal silicon dioxide.
  • the unit dose form comprises about 1 weight percent of the glidant (e.g., colloidal silicon dioxide).
  • the unit dose form further comprises a lubricant.
  • the lubricant is magnesium stearate.
  • the unit dose form comprises about 1 weight percent of the lubricant (e.g., magnesium stearate).
  • Other examples of lubricants are described in Example 13 herein.
  • the pharmaceutical composition further comprises a disintegrant.
  • the disintegrant is partly
  • pregelatinized starch low-substituted hydroxyl propyl cellulose or carmellose calcium.
  • Other examples of disintegrants are described in Example 13 herein.
  • the unit dose form is in the form of a capsule for oral administration, e.g., a hydroxypropylmethylcellulose capsule.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof are formulated into other oral dosage forms.
  • Oral dosage forms include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol.
  • push-fit capsules contain the active ingredients in admixture with one or more fillers.
  • Fillers include, by way of example only, lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers.
  • soft capsules contain the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, dissolved or suspended in a suitable liquid.
  • suitable liquids include, by way of example only, one or more fatty oil, liquid paraffin, or liquid polyethylene glycol.
  • stabilizers are optionally added.
  • compositions described herein are formulated in any conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compound(s) into preparations which can be used pharmaceutically.
  • the formulation of the pharmaceutical composition facilitates administration to a subject.
  • compositions described herein are manufactured in a conventional manner, such as, by way of example only, by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or compression processes.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is mixed with an excipient and, optionally, a lubricant and a glidant using direct blending techniques, and capsules are filled with the resulting mixture on a manual capsule filling machine.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • the excipient and the optional glidant are put through a 500 ⁇ m screen, then mixed together, and blended for 16 minutes at 30 rpm.
  • the optional lubricant is then sieved through a 250 ⁇ m screen and added to the mixture.
  • the resulting mixture is then blended for 5 minutes at 30 rpm.
  • Capsules are then filled using an overage of from 0% to about 5% (e.g., about 1%), using tamping and/or tapping, as needed.
  • pharmaceutical preparations for oral use are obtained by mixing one or more solid excipients with the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as: for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others, such as polyvinylpyrrolidone (PVP or povidone) or calcium phosphate.
  • fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol
  • cellulose preparations such as: for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others, such as polyvinylpyrrolidone (PVP or povidone) or calcium phosphate.
  • PVP polyvin
  • disintegrating agents are optionally added.
  • Disintegrating agents include, by way of example only, cross-linked croscarmellose sodium, polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
  • the compound having structure (I) e.g., a crystalline form and/or polymorph of a compound having structure (I)
  • a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof can encompass unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as, for example, ethanol, and the like.
  • the solvated forms of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, are also considered to be disclosed herein.
  • compositions optionally include other medicinal or pharmaceutical agents, carriers, adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure, buffers, and/or other therapeutically valuable substances.
  • adjuvants such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure, buffers, and/or other therapeutically valuable substances.
  • compositions comprising the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, include formulating with one or more inert, pharmaceutically acceptable excipients or carriers to form a solid, semi-solid or liquid.
  • Solid compositions include powders, tablets, dispersible granules, capsules, cachets, and suppositories.
  • Liquid compositions include solutions in which the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is dissolved, emulsions comprising the compound having structure (I), or a tautomer,
  • compositions include gels, suspensions and creams.
  • the form of the pharmaceutical compositions described herein include liquid solutions or suspensions, solid forms suitable for solution or suspension in a liquid prior to use, or as emulsions. These compositions also optionally contain minor amounts of nontoxic, auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, and so forth.
  • the pharmaceutical composition comprising the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, takes the form of a liquid where the agents are present in solution, in suspension or both.
  • a liquid composition includes a gel formulation.
  • the liquid composition is aqueous.
  • useful aqueous suspensions contain one or more polymers as suspending agents.
  • Useful polymers include water-soluble polymers, such as cellulosic polymers, e.g., hydroxypropylmethylcellulose, and water-insoluble polymers, such as cross-linked carboxyl-containing polymers.
  • Certain pharmaceutical compositions described herein comprise a mucoadhesive polymer, selected, for example, from carboxymethylcellulose, carbomer (acrylic acid polymer),
  • Useful pharmaceutical compositions also, optionally, include solubilizing agents to aid in the solubility of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
  • solubilizing agent generally includes agents that result in formation of a micellar solution or a true solution of the agent.
  • Certain acceptable nonionic surfactants for example, polysorbate 80, are useful as solubilizing agents, as are ophthalmically acceptable glycols, polyglycols, e.g., polyethylene glycol 400, and glycol ethers.
  • compositions optionally include one or more pH adjusting agents or buffering agents, including acids, such as acetic, boric, citric, lactic, phosphoric and hydrochloric acids; bases such as sodium hydroxide, sodium phosphate, sodium borate, sodium citrate, sodium acetate, sodium lactate and tris- hydroxymethylaminomethane; and buffers such as citrate/dextrose, sodium bicarbonate and ammonium chloride.
  • acids such as acetic, boric, citric, lactic, phosphoric and hydrochloric acids
  • bases such as sodium hydroxide, sodium phosphate, sodium borate, sodium citrate, sodium acetate, sodium lactate and tris- hydroxymethylaminomethane
  • buffers such as citrate/dextrose, sodium bicarbonate and ammonium chloride.
  • acids, bases and buffers are included in an amount required to maintain pH of the composition in an acceptable range.
  • compositions also, optionally, include one or more salts in an amount required to bring osmolality of the composition into an acceptable range.
  • salts include those having, for example, sodium, potassium or ammonium cations and chloride, citrate, ascorbate, borate, phosphate, bicarbonate, sulfate, thiosulfate or bisulfite anions; suitable salts include sodium chloride, potassium chloride, sodium thiosulfate, sodium bisulfite and ammonium sulfate.
  • compositions optionally include one or more preservatives to inhibit microbial activity.
  • Suitable preservatives include mercury-containing substances such as merfen and thiomersal; stabilized chlorine dioxide; and quaternary ammonium compounds such as benzalkonium chloride, cetyltrimethylammonium bromide and cetylpyridinium chloride.
  • compositions include one or more surfactants to enhance physical stability or for other purposes.
  • Suitable nonionic surfactants include polyoxyethylene fatty acid glycerides and vegetable oils, e.g., polyoxyethylene (60) hydrogenated castor oil; and polyoxyethylene alkylethers and alkylphenyl ethers, e.g., octoxynol 10, octoxynol 40.
  • compositions include one or more antioxidants to enhance chemical stability where required.
  • Suitable antioxidants include, by way of example only, ascorbic acid and sodium metabisulfite.
  • aqueous suspension compositions are packaged in single-dose non-reclosable containers. Alternatively, multiple-dose, reclosable containers are used, in which case it is typical to include a preservative in the composition.
  • other delivery systems for hydrophobic pharmaceutical compounds are employed. Liposomes and emulsions are examples of delivery vehicles or carriers useful herein. In certain embodiments, organic solvents such as N-methylpyrrolidone are also employed.
  • the compounds described herein are delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the active. Various sustained-release materials are useful herein. In some embodiments, sustained-release capsules release the active for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the active, additional strategies for protein stabilization are employed.
  • the formulations described herein comprise one or more antioxidants, metal chelating agents, thiol-containing compounds and/or other general stabilizing agents.
  • stabilizing agents include: (a) about 0.5% to about 2% w/v glycerol, (b) about 0.1% to about 1% w/v methionine, (c) about 0.1% to about 2% w/v monothioglycerol, (d) about 1 mM to about 10 mM EDTA, (e) about 0.01% to about 2% w/v ascorbic acid, (f) 0.003% to about 0.02% w/v polysorbate 80, (g) 0.001% to about 0.05% w/v.
  • polysorbate 20 (h) arginine, (i) heparin, (j) dextran sulfate, (k) cyclodextrins, (l) pentosan polysulfate and other heparinoids, (m) divalent cations such as magnesium and zinc; or (n) combinations thereof.
  • the concentration of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, provided in a pharmaceutical composition or unit dose form is no more than 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19%, 18%, 17%, 16%, 15%,14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002%, or 0.0001% w/w
  • the concentration of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is in the range of from approximately 0.0001% to approximately 50%, approximately 0.001% to approximately 40 %, approximately 0.01% to approximately 30%, approximately 0.02% to approximately 29%, approximately 0.03% to approximately 28%, approximately 0.04% to approximately 27%, approximately 0.05% to
  • the concentration of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is in the range of from approximately 0.001% to approximately 10%, approximately 0.01% to approximately 5%, approximately 0.02% to approximately 4.5%, approximately 0.03% to approximately 4%, approximately 0.04% to approximately 3.5%,
  • the amount of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, provided in a pharmaceutical composition or unit dose form is no more than 10 g, 9.5 g, 9.0 g, 8.5 g, 8.0 g, 7.5 g, 7.0 g, 6.5 g, 6.0 g, 5.5 g, 5.0 g, 4.5 g, 4.0 g, 3.5 g, 3.0 g, 2.5 g, 2.0 g, 1.5 g, 1.0 g, 0.95 g, 0.9 g, 0.85 g, 0.8 g, 0.75 g, 0.7 g, 0.65 g, 0.6 g, 0.55 g, 0.5 g, 0.45 g, 0.4 g, 0.35 g, 0.3 g, 0.25 g, 0.2 g, 0.15 g, 0.1 g, 0.09 g, 0.08 g, 0.07 g, 0.06 g
  • Embodiments of the present disclosure include methods for treating a disease associated with overexpression of a cyclin-dependent kinase (CDK), such as CDK 9, 1, 2, 4 or 7 (e.g., CDK9), in a mammal in need thereof, comprising
  • CDK cyclin-dependent kinase
  • the disease associated with overexpression of a CDK is cancer.
  • Some embodiments include methods for treatment of cancer comprising administering an effective amount of a compound having structure (I) (e.g., a crystalline form and/or polymorph thereof), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, to a subject in need thereof.
  • Certain embodiments provide a method for treatment of cancer, the method comprising administering an effective amount of a pharmaceutical composition comprising a compound having structure (I) (e.g., a crystalline form and/or polymorph thereof), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, to a subject in need thereof.
  • the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof may be used singly or in combination with one or more therapeutic agents, for example, as components of one or more mixtures.
  • the cancer treated is a hematologic cancer.
  • Hematologic malignancies that can be treated with a compound having structure (I), or a tautomer or zwitterionic form thereof, include leukemias and lymphomas.
  • the hematologic cancer is selected from acute myelogenous leukemia (AML), follicular lymphoma, acute lymphoblastic leukemia (ALL), chronic
  • the hematological cancer is AML.
  • the hematologic cancer is CLL.
  • the hematologic cancer is MM.
  • the hematologic cancer is myelodysplasic syndrome (MDS).
  • the cancer comprises a solid tumor.
  • the cancer is a solid tumor cancer.
  • the solid tumor cancer is breast cancer, bladder cancer, liver cancer, pancreatic cancer, lung cancer, colorectal cancer, ovarian cancer, prostate cancer, or melanoma.
  • the cancer is bladder cancer.
  • the cancer is lung cancer.
  • the cancer is liver cancer.
  • the cancer is a sarcoma, bladder cancer or renal cancer.
  • the cancer is prostate cancer (e.g., castration-resistant prostate cancer, castration-sensitive prostate cancer).
  • the cancer is bladder cancer, pancreatic cancer, colorectal cancer, kidney cancer, non-small cell lung carcinoma, prostate cancer, sarcoma, skin cancer, thyroid cancer, testicular cancer or vulvar cancer.
  • the cancer is endometrial cancer, pancreatic cancer, testicular cancer, renal cancer, melanoma, colorectal cancer, thyroid cancer, bladder cancer, pancreatic cancer, vulvar cancer, sarcoma, prostate cancer, lung cancer or anal cancer.
  • the cancer is a sarcoma.
  • the cancer is a renal cell carcinoma.
  • Progression-resistant prostate cancer refers to prostate cancer that progresses in a subject following administration of one or more androgen depletion therapies (ADTs). Progression of prostate cancer can be evidenced by, for example, a prostate-specific antigen doubling time (PSADT) of less than or equal to 10 months, the progression of pre-existing disease (e.g., radiographic progression, clinical progression, a skeletal-related event, prostate-specific antigen (PSA) progression), and/or the appearance of new metastases in a subject, and is typically driven by androgens, which are a class of hormones including testosterone and dihydrotestosterone (DHT).
  • PSADT prostate-specific antigen doubling time
  • DHT dihydrotestosterone
  • ADT refers to a therapy to suppress androgen levels (e.g., surgical castration or chemical castration) or androgen signaling (e.g., by reducing androgen binding to androgen receptor), which may be used to slow the progression of prostate cancer.
  • Androgen deprivation therapy typically causes a temporary reduction in tumor burden
  • Castration resistance can be biochemically characterized before the onset of symptoms by a rising titer of serum PSA (Miller, et al., 1992 J. Urol.147, 956961). Radiographic
  • progression can be assessed with the use of sequential imaging, and is evidenced by, for example, bone scan identification of two or more new bone lesions with confirmation (according to the Prostate Cancer Clinical Trials Working Group 2 criteria).
  • Response Evaluation Criteria in Solid Tumors (RECIST v 1.1) criteria can also be used to assess radiographic progression of soft tissue lesions.
  • Guidelines for monitoring prostate cancer, including progression of prostate cancer, are described in NCCN Clinical Practice Guidelines in Oncology: Prostate Cancer, version 4.2019, August 19, 2019, the relevant contents of which are incorporated herein by reference in their entirety.
  • Crop-resistant prostate cancer is used interchangeably herein with“androgen- resistant prostate cancer”,“androgen-independent prostate cancer” and“hormone-resistant prostate cancer”.
  • “Castration-sensitive prostate cancer” refers to prostate cancer that does not progress (e.g., responds) following administration of one or more ADTs. Progression of prostate cancer can be assessed according to criteria described herein, for example, with respect to“castration-resistant prostate cancer,” and guidelines for monitoring prostate cancer, including progression of prostate cancer, are described in NCCN Clinical Practice Guidelines in Oncology: Prostate Cancer, version 4.2019, August 19, 2019, the relevant contents of which are incorporated herein by reference in their entirety.“Castration-sensitive prostate cancer” is used interchangeably herein with “androgen-sensitive prostate cancer”,“androgen-dependent prostate cancer” and “hormone-sensitive prostate cancer”.
  • cancers treatable according to the methods described herein include, but are not limited to, Acute Lymphoblastic Leukemia (ALL); Acute Myeloid Leukemia (AML); Adrenocortical Carcinoma; Adrenocortical Carcinoma, Childhood; AIDS-Related Cancer (e.g., Kaposi Sarcoma, AIDS-Related Lymphoma, Primary CNS Lymphoma); Anal Cancer; Appendix Cancer; Astrocytomas, Childhood; Atypical Teratoid/Rhabdoid Tumor, Childhood, Central Nervous System; Basal Cell Carcinoma of the Skin; Bile Duct Cancer; Bladder Cancer; Bladder Cancer, Childhood; Bone Cancer (including Ewing Sarcoma, Osteosarcoma and Malignant Fibrous Histiocytoma); Brain Tumors/Cancer; Breast Cancer; Burkitt Lymphoma; Carcinoid Tumor (Gastrointestinal); Carcinoid Tumor, Childhood; Cardi
  • Esophageal Cancer Esthesioneuroblastoma; Ewing Sarcoma; Extracranial Germ Cell Tumor, Childhood; Extragonadal Germ Cell Tumor; Eye Cancer; Childhood Intraocular Melanoma; Intraocular Melanoma; Retinoblastoma; Fallopian Tube Cancer; Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma; Gallbladder Cancer; Gastric (Stomach) Cancer; Childhood Gastric (Stomach) Cancer; Gastrointestinal Carcinoid Tumor; Gastrointestinal Stromal Tumors (GIST); Childhood Gastrointestinal Stromal Tumors; Germ Cell Tumors; Childhood Central Nervous System Germ Cell Tumors (e.g., Childhood Extracranial Germ Cell Tumors, Extragonadal Germ Cell Tumors, Ovarian Germ Cell Tumors, Testicular Cancer); Gestational Trophoblastic Disease; Hairy Cell Leukemia; Head and Neck Cancer; Heart Tumors, Childhood;
  • Carcinoma Mesothelioma, Malignant; Childhood Mesothelioma; Metastatic Cancer; Metastatic Squamous Neck Cancer with Occult Primary; Midline Tract Carcinoma With NUT Gene Changes; Mouth Cancer; Multiple Endocrine Neoplasia Syndromes; Multiple Myeloma/Plasma Cell Neoplasms; Mycosis Fungoides; Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasms; Myelogenous Leukemia, Chronic (CML); Myeloid Leukemia, Acute (AML); Myeloproliferative Neoplasms, Chronic; Nasal Cavity and Paranasal Sinus Cancer; Nasopharyngeal Cancer;
  • Neuroblastoma Non-Hodgkin Lymphoma; Non-Small Cell Lung Cancer; Oral Cancer, Lip and Oral Cavity Cancer and Oropharyngeal Cancer; Osteosarcoma and Malignant Fibrous Histiocytoma of Bone; Ovarian Cancer; Childhood Ovarian Cancer; Pancreatic Cancer; Childhood Pancreatic Cancer; Pancreatic Neuroendocrine Tumors;
  • Papillomatosis (Childhood Laryngeal); Paraganglioma; Childhood Paraganglioma; Paranasal Sinus and Nasal Cavity Cancer; Parathyroid Cancer; Penile Cancer;
  • Pharyngeal Cancer Pheochromocytoma; Childhood Pheochromocytoma; Pituitary Tumor; Plasma Cell Neoplasm/Multiple Myeloma; Pleuropulmonary Blastoma;
  • Stomach Gastric Cancer
  • Childhood Stomach Gastric Cancer
  • T-Cell Lymphoma Cutaneous (e.g., Mycosis Fungoides and Sézary Syndrome); Testicular Cancer;
  • Throat Cancer e.g., Nasopharyngeal Cancer
  • Oropharyngeal Cancer Hypopharyngeal Cancer
  • Thymoma and Thymic Carcinoma Thyroid Cancer
  • Transitional Cell Cancer of the Renal Pelvis and Ureter Ureter and Renal Pelvis, Transitional Cell Cancer
  • Urethral Cancer Uterine Cancer, Endometrial
  • Uterine Sarcoma Vaginal Cancer; Childhood Vaginal Cancer; Vascular Tumors;
  • the cancer is a metastatic cancer. In other embodiments, the cancer is a primary cancer.
  • the cancer is MCL-1 dependent.
  • MCL-1-dependent refers to the subset of cancers (e.g., hematologic cancers) wherein myeloid cell leukemia 1 (MCL-1) is the primary driver of suppressing apoptosis.
  • MCL-1 dependency promotes blast survival, and is associated with treatment resistance and relapse.
  • MCL-1 dependence can be assessed, for example, by contacting a subject’s cancer cell with a profiling peptide, as described in International Publication Nos. WO 2016/172214 and WO 2018/119000, the relevant contents of which are incorporated herein by reference in their entireties.
  • the cancer is c-Myc-altered.
  • c-Myc- altered refers to the subset of cancers wherein c-Myc is altered compared to its native sequence, where its expression is amplified compared to an appropriate control (e.g., corresponding normal cells), and where protein levels suggest overexpression of c-Myc.
  • an appropriate control e.g., corresponding normal cells
  • protein levels suggest overexpression of c-Myc.
  • c-Myc drives androgen independence in prostate cancer, and overexpression attenuates the anti-tumor activity of androgen receptor suppression.
  • c-Myc is significantly upregulated in androgen receptor- sensitive prostate cancer.
  • lymphoma e.g., Burkitt lymphoma, B-cell lymphoma, T-cell lymphoma
  • cervical cancer colon cancer
  • ovarian cancer breast cancer
  • breast cancer lung cancer
  • prostate cancer colorectal cancer
  • pancreatic cancer gastric cancer and uterine cancer.
  • the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, the pharmaceutical composition, or the unit dose form is administered orally.
  • Some embodiments provide methods for combination therapies in which an agent known to modulate other pathways, or other components of the same pathway, or even overlapping sets of target enzymes are used in combination with a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
  • a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof includes the combination of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, with a chemotherapeutic agent, therapeutic antibody, and/or radiation treatment, e.g., to provide a synergistic or additive therapeutic effect.
  • chemotherapeutics are presently known in the art and can be used in combination with a compound having structure (I), or a pharmaceutically acceptable salt or zwitterionic form thereof.
  • the chemotherapeutic is selected from the group consisting of mitotic inhibitors, alkylating agents, anti- metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, biological response modifiers, anti-hormones, angiogenesis inhibitors, and anti-androgens.
  • the further therapeutic agent may comprise an alkylating agent, such as chlorambucil, cyclophosphamide, cisplatin; a mitotic inhibitor such as docetaxel (Taxotere; 1,7b,10b-trihydroxy-9-oxo-5b,20-epoxytax-11-ene-2a,4,13a-triyl 4-acetate 2-benzoate 13- ⁇ (2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-3- phenylpropanoate ⁇ ) or paclitaxel; an antimetabolite such as 5-fluorouracil, cytarabine, methotrexate, or pemetrexed; an anti-tumor antibiotic such as daunorubicin or doxorubicin; a corticosteroid such as prednisone or methylprednisone; or a Bcl-2 inhibitor such as venetoclax.
  • an alkylating agent such as chlor
  • the further therapeutic agent is docetaxel.
  • Docetaxel (trade name TAXOTERE®) is a type of chemotherapeutic agent known as an antimicrotubule agent.
  • Docetaxel is used for treating a variety of cancers, such as metastatic prostate cancer. Docetaxel treatment is often administered intravenously, and often includes premedication with a corticosteroid such as prednisone.
  • the further therapeutic agent is venetoclax (GDC-0199, ABT199, RG7601, trade name VENCLEXTA® or
  • VENCLYXTO® which is a Bcl-2 inhibitor that can induce apoptosis in cancer cells.
  • Venetoclax is typically administered orally.
  • the further therapeutic agent may be a pharmacological agent that is currently approved by the Food and Drug Administration (FDA) in the U.S. (or elsewhere by any other regulatory body) for use as pharmacological treatment of prostate cancer, or is currently being used experimentally as part of a clinical trial program that relates to prostate cancer.
  • FDA Food and Drug Administration
  • the further therapeutic agents may comprise, without limitation, the chemical entity known as enzalutamide or MDV3100 (4-(3-(4-cyano-3-(trifluoromethyl)phenyl)-5,5-dimethyl-4-oxo-2-thioxoimidazolidin-1- yl)-2-fluoro-N-methylbenzamide) and related compounds; the chemical entity known as TOK 001 and related compounds; the chemical entity known as ARN-509; the chemical entity known as abiraterone (or CB-7630; (3S,8R,9S,10R,13S,14S)-10,13-dimethyl-17- (pyridin-3-yl) 2,3,4,7,8,9,10,11,12,13,14,15-dodecahydro-1H- cyclopenta[a]phenanthren-3-ol), and related molecules; the chemical entity known as bicalutamide (N-[4-cyano-3-(trifluoromethyl)phenyl]
  • the further therapeutic agent is an androgen receptor antagonist that blocks androgen binding to androgen receptor.
  • therapies that block androgen binding to androgen receptor include enzalutamide and apalutamide.
  • the further therapeutic agent is enzalutamide.
  • Enzalutamide (trade name XTANDI®) is an androgen receptor (AR) antagonist that is used for treating non-metastatic castration-resistant prostate cancer and metastatic castration- resistant prostate cancer. Enzalutamide treatment may be combined with castration (surgical or chemical).
  • the further therapeutic agent is abiraterone.
  • Abiraterone (trade name ZYTIGA®) is a CYP17A1 inhibitor, which significantly decreases testosterone production.
  • Abiraterone treatment may be combined with other further therapies, such as a corticosteroid (e.g., prednisone) and/or castration (surgical or chemical).
  • the further therapeutic agent is selected from at least one of: a bromodomain inhibitor, a histone methyltransferase inhibitor, a histone deacetylase inhibitor, or a histone demethylases inhibitor.
  • the further therapeutic agent is a bromodomain inhibitor, for example, an inhibitor of a bromodomain protein such as Brd2, Brd3, Brd4 and/or BrdT.
  • the further therapeutic agent comprises a BRD4 inhibitor.
  • the further therapeutic agent is JQ-1 (Nature 2010 Dec 23;468(7327):1067-73), BI2536 (ACS Chem. Biol. 2014 May 16;9(5):1160-71; Boehringer Ingelheim), TG101209 (ACS Chem. Biol.2014 May 16;9(5):1160-71), OTX015 (Mol. Cancer Ther. November 201312; C244;
  • IBET762 J Med Chem.2013 Oct 10;56(19):7498-500; GlaxoSmithKline
  • IBET151 Bioorg. Med. Chem. Lett.2012 Apr 15;22(8):2968-72; GlaxoSmithKline
  • PFI-1 J. Med. Chem.2012 Nov 26;55(22):9831-7; Cancer Res.2013 Jun
  • the BRD inhibitor is IBET 762 (GSK525762), TEN-010 (Tensha Therapeutics), CPI-203 (Leukemia.28 (10): 2049–59, 2014), RVX- 208 (Proceedings of the National Academy of Sciences of the United States of America.
  • the further therapeutic agent is a histone methyltransferase inhibitor.
  • the further therapeutic agent comprises a DOT1-like histone methyltransferase (DOT1L) inhibitor.
  • DOT1L is a histone methyltransferase enzyme that targets lysine 79 in the globular domain of histone H3 for mono-, di-, or trimethylation.
  • the further therapeutic agent is EPZ004777, EPZ-5676 (Blood.2013 Aug
  • the further therapeutic agent is a histone deacetylase (HDAC) inhibitor.
  • HDAC proteins may be grouped into classes based on homology to yeast HDAC proteins with Class I made up of HDAC1, HDAC2, HDAC3 and HDAC 8; Class IIa made up of HDAC4, HDAC5, HDAC7 and HDAC 9; Class IIb made up of HDAC6 and HDAC10; and Class IV made up of HDAC11.
  • the further therapeutic agent is trichostatin A, vorinostat (Proc. Natl. Acad. Sci. U.S.A.1998 Mar 17;95(6):3003-7), givinostat, abexinostat (Mol. Cancer Ther.2006 May;5(5):1309-17), belinostat (Mol. Cancer Ther.2003
  • panobinostat Clin. Cancer Res.2006 Aug 1;12(15):4628-35
  • resminostat Clin. Cancer Res.2013 Oct 1;19(19):5494-504
  • quisinostat Clin. Cancer Res.2013 Aug 1;19(15):4262-72
  • depsipeptide Blood.2001 Nov 1;98(9):2865-8
  • entinostat Proc. Natl. Acad. Sci. U.S.A.1999 Apr 13;96(8):4592-7
  • mocetinostat Bioorg. Med. Chem.
  • the further therapeutic agent is panobinostat.
  • the further therapeutic agent is panobinostat or SAHA.
  • the further therapeutic agent is a histone demethylase inhibitor.
  • the histone demethylase inhibitor is a lysine-specific demethylase 1A (Lsd1) inhibitor.
  • the further therapeutic agent is HCI-2509 (BMC Cancer.2014 Oct 9;14:752), tranylcypromine or ORY-1001 (J. Clin. Oncol 31, 2013 (suppl; abstr e13543).
  • the further therapeutic agent is HCI-2509.
  • the further therapeutic agent is a MLL-menin inhibitor.
  • Menin is a co-factor of the oncogenic MLL fusion protein, and an MLL-menin inhibitor blocks the interaction of the two proteins.
  • MLL- menin inhibitors include MI-453, M-525, and MI-503.
  • the further therapeutic agent is a B- cell receptor signaling antagonist (e.g., a Bruton’s tyrosine kinase (BTK) inhibitor, such as ibrutinib).
  • a B- cell receptor signaling antagonist e.g., a Bruton’s tyrosine kinase (BTK) inhibitor, such as ibrutinib.
  • the further therapeutic agents is an immunomodulator.
  • Immunomodulators of particular interest for use in combination with compounds of the present disclosure include: afutuzumab (available from
  • ROCHE® pegfilgrastim
  • NEULASTA® lenalidomide
  • thalidomide thalidomide
  • actimid CC4047
  • IRX-2 mixture of human cytokines including interleukin 1, interleukin 2, and interferon g, CAS 951209-71-5, available from IRX Therapeutics.
  • the further therapeutic agent comprises a chimeric antigen receptor T-cell (CAR-T) therapy.
  • CAR-T therapies of particular interest for use in combination with compounds of the present disclosure include: tisagenlecleucel (Novartis), axicabtagene ciloleucel (Kite), and tocilizumab and atlizumab (Roche).
  • the further therapeutic agent is an immune checkpoint inhibitor (e.g., a PD-1 inhibitor, such as pembrolizumab or nivolumab; a PD-L1 inhibitor, such as atezolizumab, avelumab, or durvalumab; a CTLA-4 inhibitor; a LAG-3 inhibitor; or a Tim-3 inhibitor).
  • an immune checkpoint inhibitor e.g., a PD-1 inhibitor, such as pembrolizumab or nivolumab
  • a PD-L1 inhibitor such as atezolizumab, avelumab, or durvalumab
  • CTLA-4 inhibitor a CTLA-4 inhibitor
  • LAG-3 inhibitor LAG-3 inhibitor
  • Tim-3 inhibitor e.g., Tim-3 inhibitors, Tim-3 inhibitors.
  • Other immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure include: PD-1 inhibitors, such as pembrolizumab (KEYTRUDA®), nivoluma
  • PD-L1 inhibitors such as atezolizumab (TECENTRIQ®), avelumab (BAVENCIO®), durvalumab (IMFINZI®), FAZ053 (Novartis), and BMS-936559 (Bristol-Myers Squibb); and drugs that target CTLA-4, such as ipilimumab (YERVOY®).
  • the immune checkpoint inhibitor is a PD-1 inhibitor.
  • the PD-1 inhibitor is pembrolizumab, nivolumab, or a combination thereof.
  • the PD-1 inhibitor is pembrolizumab (also known as lambrolizumab, MK-3475, MK03475, SCH-900475, or
  • the PD-1 inhibitor is nivolumab (also known as MDX-1106, MDX-1106-04, ONO-4538, BMS-936558, or OPDIVO®).
  • nivolumab also known as MDX-1106, MDX-1106-04, ONO-4538, BMS-936558, or OPDIVO®.
  • Nivolumab (clone 5C4) and other anti-PD-1 antibodies are disclosed in US 8,008,449 and WO 2006/121168, incorporated by reference in their entireties.
  • the PD-1 inhibitor is AMP-224 (Amplimmune), CBT-501 (CBT Pharmaceuticals), CBT-502 (CBT Pharmaceuticals), JS001 (Junshi Biosciences), IBI308 (Innovent Biologics), INCSHR1210 (Incyte), also known as SHR-1210 (Hengrui Medicine), BGBA317 (Beigene), BGB-108 (Beigene), BAT-I306 (Bio-Thera Solutions), GLS-010 (Gloria Pharmaceuticals; WuXi Biologics), AK103, AK104, AK105 (Akesio Biopharma;
  • MEDI0680 Medimmune
  • PDF001 Novartis
  • PF-06801591 Pfizer
  • pidilizumab CureTech
  • REGN2810 REGN2810
  • TSR-042 Tesaro
  • CS1003 CStone Pharmaceuticals
  • MEDI0680 Medimmune
  • AMP-514 MEDI0680 and other anti- PD-1 antibodies are disclosed in US 9,205,148 and WO 2012/145493, incorporated by reference in their entireties.
  • Pidilizumab is also known as CT-011.
  • Pidilizumab and other anti-PD-1 antibodies are disclosed in Rosenblatt, J., et al. (2011) J Immunotherapy 34(5): 409-18, US 7,695,715, US 7,332,582, and US 8,686,119, incorporated by reference in their entireties.
  • the anti-PD-1 antibody molecule is cemiplimab. In one embodiment, the anti-PD-1 antibody molecule is sintilimab. In one embodiment, the anti-PD-1 antibody molecule is toripalimab. In one embodiment, the anti-PD-1 antibody molecule is camrelizumab.
  • anti-PD-1 antibody molecules include those described, e.g., in WO 2015/112800, WO 2016/092419, WO 2015/085847, WO 2014/179664, WO 2014/194302, WO 2014/209804, WO 2015/200119, US 8,735,553, US 7,488,802, US 8,927,697, US 8,993,731, and US 9,102,727, incorporated by reference in their entireties.
  • the PD-1 inhibitor is an anti-PD-1 antibody molecule as described in US 2015/0210769.
  • the anti-PD-1 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP049- Clone-E or BAP049-Clone-B disclosed in US 2015/0210769.
  • the antibody molecules described herein can be made by vectors, host cells, and methods described in US 2015/0210769, incorporated by reference in its entirety.
  • the PD-1 inhibitor is a peptide that inhibits the PD-1 signaling pathway, e.g., as described in US 8,907,053, incorporated by reference in its entirety.
  • the PD-1 inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PD-L1 or PD- L2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence).
  • the PD-1 inhibitor is AMP-224 (B7-DCIg (Amplimmune), e.g., disclosed in WO 2010/027827 and WO 2011/066342, incorporated by reference in their entireties).
  • the immune checkpoint inhibitor is a PD-L1 inhibitor.
  • the PD-L1 inhibitor is atezolizumab, avelumab, durvalumab, or a combination thereof.
  • the PD-L1 inhibitor is atezolizumab, also known as MPDL3280A, RG7446, RO5541267, YW243.55.S70, or TECENTRIQTM.
  • Atezolizumab and other anti-PD-L1 antibodies are disclosed in US 8,217,149, incorporated by reference in its entirety.
  • the PD- L1 inhibitor is avelumab, also known as MSB0010718C.
  • Avelumab and other anti-PD- L1 antibodies are disclosed in WO 2013/079174, incorporated by reference in its entirety.
  • the PD-L1 inhibitor is durvalumab, also known as MEDI4736.
  • Durvalumab and other anti-PD-L1 antibodies are disclosed in US
  • the PD-L1 inhibitor is KN035 (Alphamab; 3DMed), BMS 936559 (Bristol-Myers Squibb), CS1001 (CStone Pharmaceuticals), FAZ053 (Novartis), SHR-1316 (Hengrui Medicine), TQB2450 (Chiatai Tianqing), STI-A1014 (Zhaoke Pharm; Lee's Pharm), BGB-A333 (Beigene), MSB2311 (Mabspace Biosciences), or HLX-20 (Henlius Biotech).
  • the anti-PD-L1 antibody molecule is BMS-936559 (Bristol-Myers Squibb), also known as MDX-1105 or 12A4. BMS-936559 and other anti-PD-L1 antibodies are disclosed in US 7,943,743 and WO 2015/081158, incorporated by reference in their entireties.
  • the PD-L1 inhibitor is a monoclonal antibody (e.g., as made by Hisun Pharm and applying for clinical trials).
  • the PD-L1 inhibitor is an anti-PD-L1 antibody molecule.
  • the PD-L1 inhibitor is an anti-PD-L1 antibody molecule as disclosed in US 2016/0108123, incorporated by reference in its entirety.
  • the anti-PD-L1 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP058-Clone O or BAP058-Clone N disclosed in US 2016/0108123.
  • anti-PD-L1 antibodies include those described, e.g., in WO 2015/181342, WO 2014/100079, WO 2016/000619, WO 2014/022758, WO
  • the immune checkpoint inhibitor is a CTLA-4 inhibitor.
  • the CTLA-4 inhibitor is ipilimumab.
  • the CTLA4 inhibitor is tremelimumab.
  • the immune checkpoint inhibitor is a LAG-3 inhibitor.
  • the LAG-3 inhibitor is chosen from LAG525
  • the LAG-3 inhibitor is an anti-LAG-3 antibody molecule. In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule as disclosed in US 2015/0259420, incorporated by reference in its entirety. In one embodiment, the anti-LAG-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP050-Clone I or BAP050-Clone J disclosed in US
  • the anti-LAG-3 antibody molecule is BMS-986016 (Bristol-Myers Squibb), also known as BMS986016. BMS-986016 and other anti-LAG- 3 antibodies are disclosed in WO 2015/116539 and US 9,505,839, incorporated by reference in their entireties.
  • the anti-LAG-3 antibody molecule is TSR-033 (Tesaro).
  • the anti-LAG-3 antibody molecule is IMP731 or GSK2831781 (GSK and Prima BioMed). IMP731 and other anti-LAG-3 antibodies are disclosed in WO 2008/132601 and US 9,244,059, incorporated by reference in their entireties.
  • the anti-LAG-3 antibody molecule is IMP761 (Prima BioMed).
  • anti-LAG-3 antibodies include those described, e.g., in WO 2008/132601, WO 2010/019570, WO 2014/140180, WO 2015/116539, WO
  • the anti-LAG-3 inhibitor is a soluble LAG-3 protein, e.g., IMP321 (Prima BioMed), e.g., as disclosed in WO 2009/044273, incorporated by reference in its entirety.
  • IMP321 Primary BioMed
  • the immune checkpoint inhibitor is a TIM-3 inhibitor.
  • the TIM-3 inhibitor is MGB453 (Novartis) or TSR- 022 (Tesaro).
  • the TIM-3 inhibitor is an anti-TIM-3 antibody molecule.
  • the TIM-3 inhibitor is an anti-TIM-3 antibody molecule as disclosed in US 2015/0218274, incorporated by reference in its entirety.
  • the anti-TIM-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of ABTIM3-hum11 or ABTIM3-hum03 disclosed in US 2015/0218274.
  • the anti-TIM-3 antibody molecule is TSR-022
  • the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or light chain sequence of APE5137 or APE5121.
  • APE5137, APE5121, and other anti- TIM-3 antibodies are disclosed in WO 2016/161270, incorporated by reference in its entirety.
  • the anti-TIM-3 antibody molecule is the antibody clone F38-2E2.
  • anti-TIM-3 antibodies include those described, e.g., in WO 2016/111947, WO 2016/071448, WO 2016/144803, US 8,552,156, US 8,841,418, and US 9,163,087, incorporated by reference in their entireties.
  • cytoprotective agents such as neuroprotectants, free-radical scavengers, cardioprotectors, anthracycline extravasation neutralizers, nutrients and the like
  • Suitable cytoprotective agents include amifostine (ETHYOL®), glutamine, dimesna (TAVOCEPT®), mesna (MESNEX®), dexrazoxane (ZINECARD® or TOTECT®), xaliproden (XAPRILA®), and leucovorin (also known as calcium leucovorin, citrovorum factor and folinic acid).
  • anti-allergic agents can be administered in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti- cancer agent(s)) to minimize the risk of an allergic reaction.
  • Suitable anti-allergic agents include corticosteroids (Knutson, S., et al., PLoS One,
  • DECADRON® DECADRON®
  • beclomethasone e.g., BECLOVENT®
  • hydrocortisone also known as cortisone, hydrocortisone sodium succinate, hydrocortisone sodium phosphate, sold under the tradenames ALA-CORT®, hydrocortisone phosphate, SOLU-CORTEF®, HYDROCORT ACETATE® and LANACORT®
  • prednisolone sold under the tradenames DELTA-CORTEL®, ORAPRED®, PEDIAPRED® and PRELONE®
  • prednisone sold under the tradenames DELTASONE®, LIQUID RED®
  • methylprednisolone also known as 6- methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, sold under the tradenames DURALONE®, MEDRALONE®, MEDROL®, M- PREDNISOL® and SOLU-MEDROL®
  • antihistamines such as diphenhydramine (e.g., BENADRYL®), hydroxyzine, and cyproheptadine
  • bronchodilators such as the beta-adrenergic receptor agonists, albuterol (e.g., PROVENTIL®), and terbutaline (BRETHINE®).
  • anti-emetics can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) to prevent nausea (upper stomach) and vomiting.
  • Suitable anti-emetics include aprepitant (EMEND®), ondansetron (ZOFRAN®), granisetron HCl (KYTRIL®), lorazepam (ATIVAN®, dexamethasone (DECADRON®), prochlorperazine (COMPAZINE®), casopitant (REZONIC® and ZUNRISA®), and combinations thereof.
  • EMEND® aprepitant
  • ZOFRAN® ondansetron
  • KYTRIL® granisetron HCl
  • lorazepam ATIVAN®
  • DECADRON® dexamethasone
  • prochlorperazine COMPAZINE®
  • casopitant REZONIC® and ZUNRISA®
  • Medication to alleviate the pain experienced during treatment is often prescribed to make the patient more comfortable.
  • Common over-the-counter analgesics such TYLENOL®, can also be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)).
  • Opioid analgesic drugs such as hydrocodone/paracetamol or hydrocodone/acetaminophen (e.g., VICODIN®), morphine (e.g., ASTRAMORPH® or AVINZA®), oxycodone (e.g., OXYCONTIN® or PERCOCET®), oxymorphone hydrochloride (OPANA®), and fentanyl (e.g., DURAGESIC®) can be useful for moderate or severe pain, and can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)).
  • hydrocodone/paracetamol or hydrocodone/acetaminophen e.g., VICODIN®
  • morphine e.g., ASTRAMORPH® or AVINZA®
  • oxycodone e.g., OXYCONTIN® or PERCOCET®
  • Embodiment 1 A polymorph of a compound having the following structure (I):
  • the polymorph having an X- ray powder diffraction pattern comprising the following:
  • Embodiment 2 The polymorph of Embodiment 1, wherein the X-ray powder diffraction pattern comprises the following: D space ( ⁇ ):
  • Embodiment 3 The polymorph of Embodiment 1, wherein the X-ray powder diffraction pattern comprises the following: D space ( ⁇ ):
  • Embodiment 4 A polymorph of a compound having the following structure (I):
  • the polymorph being a crystalized form having a monoclinic space group P2 1 with lattice parameters of:
  • Embodiment 5 A polymorph of a compound having the following structure (I):
  • Embodiment 6 A polymorph of a compound having the following structure (I):
  • Embodiment 7 A polymorph of a compound having the following
  • step b) treating the product of step a) with a solvent having water content less than about 0.05 % v/v and removing the solvent, thereby forming the polymorph.
  • Embodiment 8 The polymorph of Embodiment 7, wherein the lattice forming reagent is maleic acid.
  • Embodiment 9 The polymorph of Embodiment 8, wherein the maleic acid is added at a ratio of 1:1 ⁇ 0.2 of amorphous compound to maleic acid.
  • Embodiment 10 The polymorph of any one of Embodiments 7-9, wherein the solvent is ethanol or tetrahydrofuran.
  • Embodiment 11 The polymorph of any one of Embodiments 7-10, wherein the contacting further comprises suspending the amorphous compound of structure (I) in aqueous tetrahydrofuran.
  • Embodiment 12 A polymorph of a compound having the following structure (I):
  • the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • Embodiment 13 The polymorph of Embodiment 12, wherein the subsequent purity is at least 99.5% after being stored for greater than about 7 days at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • Embodiment 14 The polymorph of Embodiment 12 or 13, wherein the subsequent purity is at least 99.5% after being stored for greater than about 30 days at about 25°C ⁇ 2°C at a relative humidity of 60%.
  • Embodiment 15 The polymorph of any one of Embodiments 12-14, wherein the initial purity and subsequent purity are as determined by HPLC.
  • Embodiment 16 A polymorph of a compound having the following structure (I):
  • polymorph has an endotherm peak value at about 256°C– 268°C as determined by differential scanning calorimetry.
  • Embodiment 17 The polymorph of Embodiment 16, wherein the endotherm peak value is at about 257.0°C– 266.0°C.
  • Embodiment 18 The polymorph of Embodiment 16 or 17, wherein the endotherm peak value is at about 258.0°C– 265.0.
  • Embodiment 19 The polymorph of any one of claims 1-18, wherein the polymorph comprises a zwitterionic form having the following structure (II): .
  • Embodiment 20 A pharmaceutical composition comprising the polymorph of any one of Embodiments 1-19 and a pharmaceutically acceptable carrier or excipient.
  • Embodiment 21 The pharmaceutical composition of Embodiment 20, wherein the pharmaceutical composition is formulated for oral administration.
  • Embodiment 22 The pharmaceutical composition of Embodiment 20 or 21, wherein the pharmaceutical composition comprises the polymorph in a
  • concentration ranging from about 0.5 wt.% to about 11.25 wt.%.
  • Embodiment 23 The pharmaceutical composition of any one of
  • Embodiments 20-22 wherein the pharmaceutical composition comprises the polymorph in a concentration ranging from about 0.6 wt.% to about 11.05 wt.%.
  • Embodiment 24 The pharmaceutical composition of any one of
  • Embodiments 20-23 wherein the pharmaceutical composition comprises about 0.6 wt.% of the polymorph.
  • Embodiment 25 The pharmaceutical composition of any one of
  • Embodiments 20-23 wherein the pharmaceutical composition comprises about 2.5 wt.% of the polymorph.
  • Embodiment 26 The pharmaceutical composition of any one of
  • Embodiments 20-23 wherein the pharmaceutical composition comprises about 11.0 wt.% of the polymorph.
  • Embodiment 27 The pharmaceutical composition of any one of
  • Embodiments 20-26 wherein the pharmaceutical composition comprises about 1 milligram (mg) of the polymorph.
  • Embodiment 28 The pharmaceutical composition of any one of
  • Embodiments 20-26 wherein the pharmaceutical composition comprises about 4 mg of the polymorph.
  • Embodiment 29 The pharmaceutical composition of any one of
  • Embodiments 20-26 wherein the pharmaceutical composition comprises about 16 mg of the polymorph.
  • Embodiment 30 The pharmaceutical composition of any one of
  • Embodiments 20-29 wherein the excipient is anhydrous lactose or microcrystalline cellulose.
  • Embodiment 31 The pharmaceutical composition of any one of
  • Embodiments 20-30 wherein the excipient is anhydrous lactose.
  • Embodiment 32 The pharmaceutical composition of any one of
  • Embodiments 20-30 wherein the excipient is microcrystalline cellulose.
  • Embodiment 33 The pharmaceutical composition of any one of
  • Embodiments 20-32 wherein the pharmaceutical composition comprises the excipient in a concentration ranging from about 85 wt.% to about 98 wt.%.
  • Embodiment 34 The pharmaceutical composition of any one of
  • Embodiments 20-33 wherein the pharmaceutical composition comprises the excipient in a concentration ranging from about 87 wt.% to about 97.5 wt.%.
  • Embodiment 35 The pharmaceutical composition of any one of
  • Embodiments 20-34 wherein the pharmaceutical composition comprises about 87 wt.% of the excipient.
  • Embodiment 36 The pharmaceutical composition of any one of
  • Embodiments 20-34 wherein the pharmaceutical composition comprises about 95.5 wt.% of the excipient.
  • Embodiment 37 The pharmaceutical composition of any one of
  • Embodiments 20-34 wherein the pharmaceutical composition comprises about 97.5 wt.% of the excipient.
  • Embodiment 38 The pharmaceutical composition of any one of
  • Embodiments 20-37 further comprising colloidal silicon dioxide.
  • Embodiment 39 The pharmaceutical composition of Embodiment 38, wherein the pharmaceutical composition comprises about 1 wt.% of the colloidal silicon dioxide.
  • Embodiment 40 The pharmaceutical composition of any one of
  • Embodiments 20-39 further comprising magnesium stearate.
  • Embodiment 41 The pharmaceutical composition of Embodiment 40, wherein the pharmaceutical composition comprises about 1 wt.% of the magnesium stearate.
  • Embodiment 42 The pharmaceutical composition of any one of
  • Embodiments 20-41 in the form of a capsule for oral administration.
  • Embodiment 43 A pharmaceutical composition comprising a polymorph of any one of Embodiments 1-19 having water content less than 0.50 % as determined by Karl Fischer titration.
  • Embodiment 44 A unit dose form comprising a pharmaceutical composition of any one of Embodiments 20-43.
  • Embodiment 45 A method for preparing a polymorph, the method comprising: a) contacting an amorphous compound having the following structure (I):
  • step b) treating the product of step a) with solvent having water content less than about 0.05 % v/v; and removing the solvent, thereby forming the polymorph.
  • Embodiment 46 The method of Embodiment 45, wherein the lattice forming reagent is an acid.
  • Embodiment 47 The method of Embodiment 46, wherein the acid is selected from the group consisting of maleic acid, fumaric acid, L-tartaric acid, hippuric acid, nicotinic acid, acetic acid, and combinations thereof.
  • Embodiment 48 The method of any one of Embodiments 45-47, wherein the lattice forming reagent is maleic acid.
  • Embodiment 49 The method of Embodiment 45, wherein the lattice forming reagent is aspartame.
  • Embodiment 50 The method of Embodiment 45, wherein the lattice forming reagent is D-xylose.
  • Embodiment 51 The method of any one of Embodiments 45-50, wherein the removing the solvent is at a pressure less than about 1 atm and a temperature greater than about 35°C.
  • Embodiment 52 The method of any one of Embodiments 45-51, wherein the method further comprises preparing a compound of structure (III):
  • Embodiment 53 The method of Embodiment 52, wherein the base is an amine base.
  • Embodiment 54 The method of Embodiment 52 or 53, wherein the base is triethylamine or diisopropylethyl amine.
  • Embodiment 55 The method of any one of Embodiments 52-54, wherein the method further comprises preparing the amorphous compound of structure (I): ,
  • Embodiment 56 The method of Embodiment 55, wherein the
  • phosphoester-cleaving compound is trimethyl silyl bromide (TMSBr), and the basic solution comprises ammonium bicarbonate.
  • Embodiment 57 The method of any one of Embodiments 45-56, wherein the polymorph is a polymorph according to any one of Embodiments 1-19.
  • Embodiment 58 A polymorph prepared according to the method of any one of Embodiments 45-57.
  • Embodiment 59 A method for treating a disease associated with overexpression of a cyclin-dependent kinase (CDK) in a mammal in need thereof, the method comprising administering a therapeutically effective amount of the polymorph of any one of Embodiments 1-19 or 58, the pharmaceutical composition of any one of Embodiments 20-43, or the unit dose form of Embodiment 43 to the mammal.
  • CDK cyclin-dependent kinase
  • Embodiment 60 The method of Embodiment 59, wherein the disease is cancer.
  • Embodiment 61 The method of Embodiment 60, wherein the cancer is a hematologic cancer.
  • Embodiment 62 The method of Embodiment 60, wherein the hematologic cancer is selected from acute myelogenous leukemia (AML), follicular lymphoma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), multiple myeloma (MM), and non-Hodgkin’s lymphoma.
  • AML acute myelogenous leukemia
  • ALL acute lymphoblastic leukemia
  • CLL chronic lymphocytic leukemia
  • MM multiple myeloma
  • non-Hodgkin’s lymphoma non-Hodgkin
  • Embodiment 63 The method of Embodiment 62, wherein the
  • hematological cancer is acute myelogenous leukemia (AML).
  • Embodiment 64 The method of Embodiment 62, wherein the hematologic cancer is chronic lymphocytic leukemia (CLL).
  • Embodiment 65 The method of Embodiment 62, wherein the hematologic cancer is myelodysplasic syndrome (MDS).
  • Embodiment 66 The method of Embodiment 62, wherein the hematologic cancer is multiple myeloma (MM).
  • MM multiple myeloma
  • Embodiment 67 The method of Embodiment 60, wherein the cancer comprises a solid tumor.
  • Embodiment 68 The method of Embodiment 60 or 67, wherein the cancer is bladder cancer.
  • Embodiment 69 The method of Embodiment 60 or 67, wherein the cancer is lung cancer.
  • Embodiment 70 The method of Embodiment 60 or 67, wherein the cancer is liver cancer.
  • Embodiment 71 The method of Embodiment 60 or 67, wherein the cancer is prostate cancer.
  • Embodiment 72 The method of any one of Embodiments 60-71, wherein the polymorph, the pharmaceutical composition, or the unit dose form is administered orally.
  • X-ray powder diffraction [00341] Stoe Stadi P. Copper KaI radiation, 40kV / 40mA; Mythen 1K detector transmission mode, curved monochromator, 0.02°2q step size, 12 s step time, 1.5- 50.5°2q scanning range with 1°2q detector step in step-scan mode.
  • XRPD X-ray powder diffraction
  • the method used to detect and determine purity of compound of structure (I) and related substances was a reverse-phase HPLC method with a gradient program and DAD detection technique.
  • the gradient program is depicted in the following table:
  • Total Impurities was calculated by summing the percentages of each individual impurity, including alvocidib. Other Impurities (%) was calculated by summing the percentages of each individual impurity, excluding alvocidib. Purity of compound of structure (I) (%) was calculated by taking the difference between 100% and the Total Impurities (%). All individual impurities at and above 0.05% were taken for the calculation of total impurities.
  • DSC Differential Scanning Calorimetry
  • DSC was performed using a TA Q200/Q2000DSC from TA Instruments using a ramp method and a crimped, aluminum sample pan at 25 °C.
  • the heating rate was 10 °C/minute, and the purge gas was nitrogen.
  • Step 1 A-1 was treated with boron tribromide in chlorobenzene. Removal of byproducts by distillation and crystallization from chlorobenzene-methanol-water resulted in A-2 as free base.
  • Step 2 A-2 (in free base form) was treated with diethyl chlorophosphate and diisopropylethylamine in N-methylpyrrolidone. Water was added to stop the reaction and precipitate the product. The resulting slurry was filtered, washed with water, and dried under vacuum to produce the compound A-3.
  • Step 3 A-3 was treated with trimethylsilyl bromide to deprotect A-3 and afford A-4 as a hydrobromide, which was treated with ammonium bicarbonate solution.
  • the precipitated A-4 i.e., compound of structure (I) having an amorphous crystal structure (i.e., "Form A" was filtered and dried.
  • Step 4 A-4 was suspended in a mixture of THF and water (19:1), and maleic acid was added. After stirring at room temperature, the solid was filtered and dried in a filter dryer to afford A-5. The resultant filtered solid compound A-5 was suspended in ethanol and re-slurried before an additional filtration. Filtered product (i.e., A-5 as polymorph form B) was washed with ethanol and dried to afford the desired product.
  • Form A amorphous form
  • DVS dynamic vapor sorption
  • Polymorph Form B (API) was formulated into two blends for four-week stability studies. Four excipients were tested in the following mixtures:
  • Step 1.1 To a clean and dry, three-necked, round-bottomed flask (RBF) (3 L) was added A-1 (90 g, 0.192 mol) and chlorobenzene (774 ml) at room temperature. To the reaction flask was slowly added BBr 3 (391.5 g) at room temperature. After completion of BBr3 addition, the temperature of the reaction mixture was slowly raised to 80-83 °C, and the reaction mixture was stirred at the same temperature for 10 hours. The reaction mixture temperature was further raised to 100-103 °C, and the reaction mixture was maintained at 100-103 °C for 5 hours. The reaction progress was monitored by TLC and HPLC.
  • HBr and methyl bromide was removed at room temperature by nitrogen bubbling into the reaction mixture, while maintaining the vigorous stirring.
  • the reaction mixture was slowly quenched with a mixture of methanol (180ml)/water (90ml) (270 ml), followed by methanol (180 ml).
  • the solvent was removed under atmospheric distillation at 25-50 °C to reach the target reaction mass volume of 12 volumes (vol).
  • the reaction mixture pH was adjusted to 3.0 ⁇ 1 using sodium hydroxide solution (48.8 g dissolved in 135 ml of DM water) at 50-55 °C. Again, the solvent was removed under
  • Step 2.1A To a clean and dry, three-necked RBF (3 L) was added A-2 (35.0 g, 0.087 mol) and DMF (245 ml), at room temperature, under nitrogen atmosphere. Then, DMAP (1.06 g, 0.0086 mol) followed by CCl4 (66.5 g 0.434mol) were added to the reaction mixture at room temperature. To the reaction mixture di-tertiary butyl phosphite (25.5g, 0.131 mol) was added at room temperature. The reaction mixture was stirred at room temperature under nitrogen atmosphere for 24 hours. The reaction progress was monitored by HPLC.
  • Step 2.1B To a clean and dry RBF (1 L) was added A-10 (51.0 g, 0.0858 mol) and acetic acid (102 ml) at room temperature. Then, 4N HCl solution in 1,4- dioxane (102 ml) was added dropwise at 25-30 °C. The reaction mixture was stirred at 25-30 °C for 40 minutes. The reaction progress was monitored by TLC. After completion of the reaction, toluene (2 ⁇ 510 ml) was added to the reaction mixture under stirring, and the reaction mixture was maintained for 5 minutes. The stirring was stopped, and the solids in the reaction mixture were allowed to settle at 25-30 °C for 5 minutes. The solvent was decanted to obtain the semi-solid.
  • Step 3.1 To a clean and dry, three-necked, 500 ml RBF was added A-11 (34.0 g, 0.066 mol) and ACN (51 ml). To the reaction mixture was dropwise added ammonium bicarbonate solution (16.2 g dissolved in 170 ml of DM water) under stirring at 25-30 °C for 30 minutes. Again, ACN (51 ml) was slowly added at 25-30 °C for 30 minutes. The reaction mixture was cooled to 10-15 °C and stirred at 10-15 °C for 60 minutes. The resulting solid was filtered and washed with ACN (102 ml). The solid was dried in a vacuum oven at 25-30 °C for 16 hours to obtain A-4 as a pale yellow solid (28.5 g, 90.10%). HPLC Purity: 99.68%.
  • Step 4.1 To a clean and dry, 500-ml, three-necked RBF was added A-4 (7.5 g, 0.015 mol) and methanol (187.5 ml) at room temperature. To the reaction mixture was slowly added acetic acid (7.5 ml, 1.0 vol) at 50 °C, under nitrogen atmosphere. The reaction mixture was stirred at 50 °C for 1 h, under nitrogen atmosphere. The reaction mixture was cooled to room temperature and stirred for 2 h. The solid was filtered and dried under vacuum to obtain 5.0 g A-5 (66.5%) as a pale yellow solid. HPLC Purity: 99.77%.
  • A-4 was treated with acetic acid (1 volume) and a solvent (25 volumes) according to the conditions listed in Table 16 to obtain A-5 as a pale yellow solid.
  • A-4 was treated with acetic acid (1 volume) and a solvent according to the conditions listed in Table 17 to obtain A-5 as a pale yellow solid. Table 17.
  • Polymorph Form B obtained using the Step 2.1B reaction conditions described in Scheme 2 was submitted to a four-week stability study to test the effects of different packing conditions on the stability of A-5.
  • Packing Condition 1 polymorph Form B was packed into an amber-colored bottle, which was closed with a rubber stopper and sealed with a flip-off aluminum cap.
  • Packing Condition 2 polymorph Form B was packed in a low-density polyethylene bag (LDPE) twisted and tied. The LDPE bag was then inserted into a black, LDPE bag along with one silica gel bag, and the black, LDPE bag was heat sealed under nitrogen atmosphere.
  • LDPE low-density polyethylene bag
  • the black, LDPE bag was then inserted into a triple-laminated aluminum bag along with one silica gel bag, and the aluminum bag was heat sealed under nitrogen atmosphere.
  • the triple- laminated aluminum bag containing polymorph Form B was kept in a high-density polyethylene container. The results of the stability study appear in Table 20. Table 20.
  • Samples were also tested for dissolution.
  • Six capsules were tested for dissolution according to the parameters outlined in Table 23. Each capsule was weighed prior to dissolution testing. The stated amount of dissolution medium was transferred into each vessel in accordance with the capsule strength under analysis. The dissolution medium was allowed to equilibrate in the dissolution bath to 37 °C ⁇ 0.5 °C. The temperature of the dissolution medium checked at the start and end of the dissolution test for each vessel. At each sample point, the solution was transferred directly into an HPLC vial.
  • the drug product Prior to encapsulation into the capsules, the drug product was made by direct blending via triturating the compound of structure (I) into the indicated excipients, followed by filling the capsules on a manual capsule filling machine in 100-capsule plates.
  • the capsules were packaged in aluminum blister packaging, with one capsule per blister and seven capsules per blister sheet. Three blisters on each sheet were left empty.
  • FIG.12 is a graph depicting completed cycles on the study through Cohort 5.
  • 3 additional patients will be enrolled and treated at that dose level.
  • up to 3 additional patients are added to a given dose level, if only 1 out of those 6 patients experiences a DLT, the dose will be increased to the next dose level. If 32 out of 3-6 patients at a dose level experience DLTs, the dose will be decreased to the previous (lower) dose level and 3 additional patients will be enrolled at that dose level.
  • the MTD is defined as the dose at which £ of 6 patients experience a DLT during Cycle 1 with the next higher dose having at least 2 of 3 to 6 patients experiencing a DLT during Cycle 1.
  • All patients may continue to receive compound of structure (I) in 21-day cycles (14 days of active treatment) at the same dose given during Cycle 1 until they experience unacceptable toxicity or unequivocal disease progression. No intra-patient escalation of the compound of structure (I) dose is permitted during the escalation phase until MTD is established.
  • Prothrombin time within 1.5x normal limits
  • aPTT Activated partial thromboplastin time
  • DLT was defined as any one of the following events observed in cycle 1, regardless of investigator attribution, unless there was a clear alternative explanation:
  • Plasma PK parameters of compound of structure (I) and alvocidib were evaluated in Cohorts 1-5 at specific timepoints during the study. Blood was collected from patients in Cohorts 1-5 according to the pharmacokinetic sampling schedule described in Table 29.
  • PK parameters were estimated using standard noncompartmental methods. Actual sample collection times were used rather than scheduled collection times.
  • Plasma concentrations below the limit of quantification were treated as 0.
  • Imbedded missing plasma concentrations e.g., missing values between two observed values
  • Other missing plasma concentrations were excluded from calculations to estimate PK parameters.
  • FIGs.11A and 11B are graphs of plasma alvocidib concentration (ng/mL) versus time, and show the concentration of alvocidib in the plasma of patients in Cohort 1 on days 1 and 14, respectively, following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • Subject 104 showed some accumulation of alvocidib after 24 hours on day 14.
  • Subject 102 was discontinued prior to day 14 dosing.
  • FIGs.11E and 11F are graphs of plasma alvocidib concentration (ng/mL) versus time, and show the concentration of alvocidib in the plasma of patients in Cohort 5 on days 1 and 14, respectively, following daily oral BID dosing with 6 mg of
  • Table 30 reports Tmax, Cmax and AUC(0-24) of alvocidib for patients in Cohort 5 on days 1 and 14 of cycle 1.
  • FIG. 11G is a graph of alvocidib (ng/mL) versus cohort, and shows the mean C max of alvocidib on day 1 and day 14 following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01.
  • FIG.11H is a graph of alvocidib (ng*hr/mL) versus cohort, and shows the area under the curve (AUC) of alvocidib on day 1 (AUC 0-8 ) and day 14 (AUC 0-8 and AUC 0-24 ) following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01. There was no detectable compound of structure (I) at any timepoint.
  • FIG.11I is a graph of mean concentration of alvocidib (nM) versus time, and shows the mean concentration of alvocidib in plasma of Cohort 5 patients over a 24-hour period.
  • A-10 was obtained according to Steps 1.1 and 2.1A, depicted in Scheme 2 and described in Example 10.
  • A-10 (100 mg) was substantially dissolved in methanol (1 ml) at 50 °C.
  • the resulting reaction mixture was stirred for one hour at room temperature, and then filtered to obtain A-5 (77.4 mg) having a crystallinity of 94%. Residual maleic acid was confirmed by 1 H NMR (0.01 proton).
  • CANCER This is a Phase 2, open-label, non-randomized, Simon 2-stage design study to establish the efficacy and safety of compound of structure (I) (e.g., Form B of compound of structure (I)) taken once daily for 21 days of a 28-day cycle in patients with metastatic castration-resistant prostate cancer who have progressed on frontline treatment with androgen signaling inhibitors.
  • a biopsy sub-study in 20 patients will enable the evaluation of tissue biomarkers in a subset of patients.
  • All patients may continue to receive compound of structure (I) in 28-day cycles (21 days of active treatment) at the same dose given during Cycle 1 until they experience unacceptable toxicity or unequivocal disease progression.
  • AST/SGOT Aspartate aminotransferase
  • ALT/SGPT alanine aminotransferase
  • aPTT Activated partial thromboplastin time
  • ICF informed consent form
  • CHF congestive heart failure
  • Enrolled patients will receive compound of structure (I) (e.g., given as a 1- mg capsule containing Formulation No.401-01, wherein the compound of structure (I) is Form B of the compound of structure (I)), administered once daily (QD) for the first 21 days of a 28-day cycle. Patients who successfully complete a 4-week treatment cycle without evidence of significant treatment-related toxicity or progressive disease will continue to receive treatment with the same dose and dosing schedule.
  • compound of structure (I) e.g., given as a 1- mg capsule containing Formulation No.401-01, wherein the compound of structure (I) is Form B of the compound of structure (I)
  • QD once daily
  • ORR objective response rate
  • DoR type of response
  • time to progression e.g., complete remission, partial remission, stable disease
  • the ORR is defined as the percent of patients with CR or PR according to PCWG3-modified RECIST v1.1 criteria, relative to the Response
  • ORR Evaluable population. ORR will be summarized by number and percentage of patients meeting the definition of ORR along with the corresponding exact 95% confidence intervals.
  • Tolerance and toxicity of oral compound of structure (I) will be assessed through evaluation of physical examinations, vital signs, laboratory parameters, AEs including DLTs, and all causes of mortality.
  • TEAEs treatment-emergent adverse events
  • MedDRA Medical Dictionary for Regulatory Activities
  • SAEs serious adverse events
  • PD parameters and assessment of potential tumor and peripheral blood biomarkers including, but not limited to, CDK9-related genes (including c-Myc) in biopsy and CTC samples; Phospho-AR; PhosphoRNAPol2 on biopsy and PBMC samples; serum PSA.
  • CDK9-related genes including c-Myc
  • Phospho-AR including c-Myc
  • PhosphoRNAPol2 on biopsy and PBMC samples
  • serum PSA serum
  • Biopsy samples will be taken at baseline (prior to dosing on Cycle 1/Day 1) and at the end of cycle two (2) in a subset of patients participating in the biopsy sub-study.

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Abstract

A crystalline form and/or polymorph of a compound having the following structure (I), including tautomeric and zwitterionic forms thereof, are provided: Methods associated with preparation and use of the polymorphs, and pharmaceutical compositions comprising the same are also provided. Also provided are methods for preparing a compound having formula (I), or a salt, tautomer or zwitterionic form thereof.

Description

CDK9 INHIBITORS AND POLYMORPHS THEREOF FOR USE AS AGENTS FOR TREATMENT OF CANCER RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Application No. 62/775,303, filed on December 4, 2018. The entire teachings of the above application is incorporated herein by reference. BACKGROUND
[0002] Alvocidib (flavopiridol) is a potent cyclin-dependent kinase (CDK) inhibitor with selectivity for CDKs 9, 1, 2, 4 and 7. 2-(2-Chlorophenyl)-5-hydroxy-8-((3S,4R)- 3-hydroxy-1-methylpiperidin-4-yl)-4-oxo-4H-chromen-7-yl dihydrogen phosphate, disclosed in International Publication No. WO 2016/187316, is an orally bioavailable prodrug of alvocidib.
[0003] There is a need for crystalline forms and/or polymorphs of 2-(2- chlorophenyl)-5-hydroxy-8-((3S,4R)-3-hydroxy-1-methylpiperidin-4-yl)-4-oxo-4H- chromen-7-yl dihydrogen phosphate that are suitable for use in pharmaceutical compositions and methods for treating diseases associated with overexpression of a CDK. There is a further need for methods for preparing 2-(2-chlorophenyl)-5-hydroxy- 8-((3S,4R)-3-hydroxy-1-methylpiperidin-4-yl)-4-oxo-4H-chromen-7-yl dihydrogen phosphate that enable the manufacture of 2-(2-chlorophenyl)-5-hydroxy-8-((3S,4R)-3- hydroxy-1-methylpiperidin-4-yl)-4-oxo-4H-chromen-7-yl dihydrogen phosphate for use in pharmaceutical compositions and methods for treating diseases associated with overexpression of a CDK. BRIEF SUMMARY
[0004] Embodiments of the present invention are generally directed to CDK (e.g., CDK9) inhibitors and polymorphs thereof as well as pharmaceutical compositions comprising the same, for use as therapeutic or prophylactic agents, for example, for treatment of cancer (e.g., hematological cancer) and other conditions. [0005] Some embodiments provide a crystalline form of a compound having the structure (I):
,
Figure imgf000004_0001
or a tautomer or zwitterionic form thereof.
[0006] More specifically, aspects of the present disclosure are directed to a polymorph of a compound having the structure (I), or a tautomer or zwitterionic form thereof. For example, in some embodiments the polymorph has an X-ray powder diffraction pattern comprising the following: D space (Å): 18.3 ± 0.09, 8.1 ± 0.06, 6.4 ± 0.08, 5.9 ± 0.06, 4.4 ± 0.05 expressed in terms of“D” spacing.
[0007] Another embodiment affords a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, the polymorph being a crystalized form having a monoclinic space group P21 with lattice parameters of a = 6.46(1) Å, b = 9.07(2) Å, c = 18.25(4) Å, b = 95.457(2)°, and a volume of 1066.11(4) Å3.
[0008] One embodiment provides a crystalline form of a compound of structure (I), or a tautomer or zwitterionic form thereof, having an x-ray powder diffraction pattern substantially in accordance with that depicted in FIG.1.
[0009] Yet another embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph is Form B as described herein.
[0010] Still another embodiment affords a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph is formed by a method comprising (a) contacting an amorphous compound of structure (I) with a lattice forming reagent; and (b) treating the product of step (a) with solvent having water content less than about 0.05% v/v and removing the solvent, thereby forming the polymorph.
[0011] One embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days at about 25°C ± 2°C at a relative humidity of 60%.
[0012] One embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof having an endotherm peak value at about 256°C– 268°C as determined by differential scanning calorimetry.
[0013] Pharmaceutical compositions comprising a compound having structure (I) (e.g., a polymorph or crystalline form of a compound having structure (I)), or a tautomer or zwitterionic form thereof, and a pharmaceutically acceptable carrier or excipient are also provided in various other embodiments. One embodiment provides a pharmaceutical composition comprising from about 0.5 weight percent to about 11.25 weight percent of a compound having the structure (I), or a tautomer or zwitterionic form thereof; and from about 85 weight percent to about 99.5 weight percent of a pharmaceutically acceptable carrier or excipient. One embodiment provides a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer or zwitterionic form thereof; about 97.4 weight percent of anhydrous lactose; about 1 weight percent colloidal silicon dioxide; and about 1 weight percent magnesium stearate. Another embodiment provides a pharmaceutical composition comprising about 11 weight percent of a compound having the structure (I), or a tautomer or zwitterionic form thereof; about 87 weight percent of anhydrous lactose; about 1 weight percent colloidal silicon dioxide; and about 1 weight percent magnesium stearate. Yet another embodiment provides a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer or zwitterionic form thereof; and from about 98 weight percent to about 99.5 weight percent of cornstarch. Another embodiment provides a pharmaceutical composition comprising about 11 weight percent of a compound of the structure (I), or a tautomer or zwitterionic form thereof; and about 88 weight percent of cornstarch.
[0014] Other embodiments provide methods including a method for treatment of a disease associated with overexpression of a cyclin-dependent kinase (CDK), such as cancer (e.g., a hematologic cancer), in a mammal in need thereof, for example, by administering to the mammal a therapeutically effective amount of a crystalline form or a polymorph of a compound having structure (I), or a tautomer or zwitterionic form thereof. [0015] In other embodiments, the present disclosure provides a method for preparing a polymorph or crystalline form of the compound of structure (I). One embodiment provides a method for preparing crystalline Form B of a compound having structure (II):
Figure imgf000006_0001
the method comprising contacting amorphous compound having the structure (I), or a tautomer or zwitterionic form thereof, with an acid in a solvent, thereby preparing the crystalline Form B of the compound having structure (II). Another embodiment provides a method for preparing crystalline Form B of the compound having structure (II), the method comprising contacting a compound having structure (V):
Figure imgf000006_0002
or a tautomer, salt or zwitterionic form thereof, with an acid in a solvent, thereby preparing the crystalline Form B of the compound having structure (II). Yet another embodiment provides a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting a compound having the following structure (IV):
Figure imgf000007_0001
or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof, in an organic solvent, with an acid having a pKa value of greater than about 1 (e.g., an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1), thereby preparing crystalline Form B of a compound having structure (II). Another embodiment is a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; contacting the compound having structure (V), or a tautomer or salt thereof, with an acid having a pKa value of less than about 1, thereby forming a salt of a compound having structure (I); contacting the salt of a compound having structure (I) with a base, thereby forming amorphous compound having structure (I); and contacting the amorphous form of the compound having structure (I), in an organic solvent, with an acid having a pKa value of greater than about 1 (e.g., an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1), thereby preparing crystalline Form B of the compound having structure (II).
[0016] The present disclosure also provides methods for preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof. The method comprises contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert-butylchlorophosphonate, di-tert- butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof, with an acid, thereby preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof.
[0017] These and other aspects of the disclosure will be apparent upon reference to the following detailed description. BRIEF DESCRIPTION OF THE DRAWINGS
[0018] In the figures, identical reference numbers identify similar elements. The sizes and relative positions of elements in the figures are not necessarily drawn to scale and some of these elements are enlarged and positioned to improve figure legibility. Further, the particular shapes of the elements as drawn are not intended to convey any information regarding the actual shape of the particular elements, and have been solely selected for ease of recognition in the figures.
[0019] FIG.1 illustrates an x-ray diffractogram obtained from XRPD analysis for polymorph Form B.
[0020] FIG.2 shows a stability profile in the form of a TG-FTIR thermogram and a DSC spectrum for the amorphous form of structure (I) (i.e., Form A).
[0021] FIG.3 illustrates a comparison of lattice forming reagents and the similarity of diffractogram patterns as determined by XRPD for polymorph Form B.
[0022] FIG.4 depicts the Oak Ridge Thermal Ellipsoid Plot (ORTEP) diagrams of single crystal structure obtained for polymorph Form B.
[0023] FIG.5 shows diffractograms from XRPD analysis of three samples of polymorph Form C.
[0024] FIG.6A-6B show TG-FTIR thermograms of polymorph Form C before (FIG.6A) and after drying (FIG.6B).
[0025] FIG.7 shows a comparison of 1H NMR spectra acquired for forms A (amorphous), form B (polymorph) and form C.
[0026] FIG.8 shows the differential scanning calorimetry output of heat flow plotted as a function of temperature for polymorph form B.
[0027] FIG.9A is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and filler in the excipient compatibility study described in Example 13. [0028] FIG.9B is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and lubricant in the excipient compatibility study described in Example 13.
[0029] FIG.9C is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and disintegrant in the excipient compatibility study described in Example 13.
[0030] FIG.9D is a graph of percentage of drug released versus time, and shows the amount of API released from various formulations of API and fluidizer/other excipient in the excipient compatibility study described in Example 13.
[0031] FIG.10A is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-01 of Example 14 stored at 5 °C.
[0032] FIG.10B is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-01 of Example 14 stored at 25 °C and 60% relative humidity (RH).
[0033] FIG.10C is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-01 of Example 14 stored at 40 °C and 75% RH.
[0034] FIG.10D is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-02 of Example 14 stored at 5 °C.
[0035] FIG.10E is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-02 of Example 14 stored at 25 °C and 60% RH.
[0036] FIG.10F is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-02 of Example 14 stored at 40 °C and 75% RH.
[0037] FIG.10G is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-03 of Example 14 stored at 5 °C. [0038] FIG.10H is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-03 of Example 14 stored at 25 °C and 60% RH.
[0039] FIG.10I is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-03 of Example 14 stored at 40 °C and 75% RH.
[0040] FIG.10J is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-04 of Example 14 stored at 5 °C.
[0041] FIG.10K is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-04 of Example 14 stored at 25 °C and 60% RH.
[0042] FIG.10L is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-04 of Example 14 stored at 40 °C and 75% RH.
[0043] FIG.10M is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-05 of Example 14 stored at 5 °C.
[0044] FIG.10N is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-05 of Example 14 stored at 25 °C and 60% RH.
[0045] FIG.10O is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-05 of Example 14 stored at 40 °C and 75% RH.
[0046] FIG.10P is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-06 of Example 14 stored at 5 °C.
[0047] FIG.10Q is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-06 of Example 14 stored at 25 °C and 60% RH. [0048] FIG.10R is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-06 of Example 14 stored at 40 °C and 75% RH.
[0049] FIG.10S is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-08 of Example 14 stored at 5 °C.
[0050] FIG.10T is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-08 of Example 14 stored at 25 °C and 60% RH.
[0051] FIG.10U is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-08 of Example 14 stored at 40 °C and 75% RH.
[0052] FIG.10V is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-09 of Example 14 stored at 5 °C.
[0053] FIG.10W is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-09 of Example 14 stored at 25 °C and 60% RH.
[0054] FIG.10X is a graph of dissolution (%) versus time, and shows the amount of compound of structure (I) released from Formulation No.401-09 of Example 14 stored at 40 °C and 75% RH.
[0055] FIG.11A is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 1 on day 1 following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01.
[0056] FIG.11B is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 1 on day 14 following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01.
[0057] FIG.11C is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 2 on day 1 following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01.
[0058] FIG.11D is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in cohort 2 on day 14 following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01.
[0059] FIG.11E is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in Cohort 5 on day 1 following daily oral BID dosing with 6 mg of Formulation No.401-01.
[0060] FIG.11F is a graph of plasma alvocidib concentration (ng/mL) versus time, and shows the concentration of alvocidib in the plasma of patients in Cohort 5 on day 14 following daily oral BID dosing with 6 mg of Formulation No.401-01.
[0061] FIG.11G is a graph of alvocidib (ng/mL) versus cohort, and shows the average Cmax of alvocidib on day 1 and day 14 following daily oral QD dosing with a 1- mg strength capsule containing Formulation No.401-01.
[0062] FIG.11H is a graph of alvocidib (ng*hr/mL) versus cohort, and shows the area under the curve (AUC) of alvocidib on day 1 (AUC0-8) and day 14 (AUC0-8 and AUC0-24) following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01.
[0063] FIG.11I is a graph of mean concentration of alvocidib (nM) versus time, and shows the mean concentration of alvocidib in plasma of Cohort 5 patients over a 24-hour period.
[0064] FIG.12 is a graph, and shows the completed cycles on the study described in Example 15 through Cohort 5. DETAILED DESCRIPTION
[0065] In the following description, certain specific details are set forth in order to provide a thorough understanding of various embodiments of the disclosure. However, one skilled in the art will understand that the disclosure may be practiced without these details.
[0066] Unless the context requires otherwise, throughout the present specification and claims, the word "comprise" and variations thereof, such as,“comprises” and “comprising” are to be construed in an open, inclusive sense (i.e., as“including, but not limited to”).
[0067] Reference throughout this specification to“one embodiment” or“an embodiment” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Thus, the appearances of the phrases "in one embodiment" or "in an embodiment" in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics may be combined in any suitable manner in one or more embodiments.
[0068] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. As used in the specification and claims, the singular form“a,”“an,” and“the” include plural referents unless the context clearly dictates otherwise.
[0069] “Crystalline,” as used herein, refers to a homogeneous solid formed by a repeating, three-dimensional pattern of atoms, ions or molecules having fixed distances between constituent parts. The unit cell is the simplest repeating unit in this pattern. Notwithstanding the homogenous nature of an ideal crystal, a perfect crystal rarely, if ever, exists.“Crystalline,” as used herein, encompasses crystalline forms that include crystalline defects, for example, crystalline defects commonly formed by manipulating (e.g., preparing, purifying) the crystalline forms described herein. A person skilled in the art is capable of determining whether a sample of a compound is crystalline notwithstanding the presence of such defects.
[0070] “Polymorph,” as used herein, refers to a crystalline form of a compound characterized by a distinct arrangement of its molecules in a crystal lattice. Polymorphs can be characterized by analytical methods such as x-ray powder diffraction (XRPD), differential scanning calorimetry (DSC) and thermogravimetric analysis.
[0071] The crystalline forms and/or polymorphs described herein can be substantially pure. As used herein,“substantially pure,” used without further qualification, means the indicated compound has a purity greater than 90 weight percent, for example, greater than 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 weight percent, and also including a purity equal to about 100 weight percent, based on the weight of the compound. The remaining material comprises other form(s) of the compound, and/or reaction impurities and/or processing impurities arising from its preparation (e.g., alvocidib). Purity can be assessed using techniques known in the art, for example, using an HPLC assay described herein.“Substantially pure” can also be qualified as in“substantially pure of other physical forms of the compound having structure (I), or a tautomer or zwitterionic form thereof” or“substantially pure of alvocidib.” When qualified thus,“substantially pure” means that the indicated compound contains less than 10%, preferably less than 5%, more preferably less than 3%, most preferably, less than 1% by weight of the indicated impurity (e.g., any other physical forms of an indicated crystalline form of a compound; alvocidib).
[0072] As used herein, the term“alvocidib” means 2-(2-chlorophenyl)-5,7- dihydroxy-8-[(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]chromen-4-one, or a salt (e.g., a pharmaceutically acceptable salt) thereof (e.g., 2-(2-chlorophenyl)-5,7-dihydroxy-8- [(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]chromen-4-one hydrochloride).
[0073] An XRPD pattern or DSC thermogram that is“substantially in accordance” with one or more figures herein showing an XRPD pattern or diffractogram or DSC thermogram, respectively, is one that would be considered by one skilled in the art to represent the same single crystalline form of the compound having structure (I), or a tautomer or zwitterionic form thereof, as the sample of the compound having structure (I), or a tautomer or zwitterionic form thereof, that provided the pattern or
diffractogram or thermogram of one or more figures provided herein. Thus, an XRPD pattern or DSC thermogram that is substantially in accordance may be identical to that of one of the figures or, more likely, may be somewhat different from one or more of the figures. For example, an XRPD pattern that is somewhat different from one or more of the figures may not necessarily show each of the lines of the diffraction pattern presented herein and/or may show a slight change in appearance or intensity of the lines or a shift in the position of the lines. These differences typically result from differences in the conditions involved in obtaining the data or differences in the purity of the sample used to obtain the data. A person skilled in the art is capable of determining if a sample of a crystalline compound is of the same form as or a different form from a form disclosed herein by comparison of the XRPD pattern or DSC thermogram of the sample and the corresponding XRPD pattern or DSC thermogram disclosed herein. [0074] The crystalline forms provided herein can also be identified on the basis of differential scanning calorimetry (DSC) and/or thermogravimetric analysis (TGA). DSC is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample is measured as a function of temperature. DSC can be used to detect physical transformations, such as phase transitions, of a sample. For example. DSC can be used to detect the temperature(s) at which a sample undergoes crystallization, melting or glass transition. It is to be understood that any temperature associated with DSC specified herein, with the exception of the DSC temperatures in the Figures or Examples, means the specified value ± 5 °C or less. For example, when an embodiment or a claim specifies an endothermic peak at 264 °C, this is to be understood to mean 264 °C ± 5 °C or less, that is a temperature of from 259 °C to 269 °C. In preferred embodiments, a DSC is the specified value ± 3 °C or less, in more preferred embodiments, ± 2 °C or less.
[0075] “Lattice forming reagent” or“salt former” refers to a chemical substance that is used in combination with another compound to facilitate the formation of a crystalline or polymorphic solid. For example, in some embodiments, a lattice forming reagent facilitates the formation of polymorph Form B of the compound of structure (I). Lattice forming reagents include acids, bases, sugars, peptides, and the like. In some embodiments, the lattice forming reagent is an acid (e.g., an acid having at least one pKa value that is less than about 5, such as about 4). For example, a lattice forming reagent may be an organic acid (e.g., maleic acid, acetic acid, fumaric acid, tartaric acid). In some embodiments, the acid is a diprotic acid.
[0076] The term“effective amount” or“therapeutically effective amount” refers to that amount of a compound (e.g., polymorph Form B of a compound of structure (I)) described herein that is sufficient to effect the intended application including disease treatment, as defined below. The therapeutically effective amount may vary depending upon the intended treatment application (in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The term also applies to a dose that will induce a particular response in target cells, e.g., reduction of platelet adhesion and/or cell migration. The specific dose will vary depending on the particular compound chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
[0077] As used herein,“treatment” or“treating” refers to an approach for obtaining beneficial or desired results with respect to a disease, disorder or medical condition including a therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated. Also, a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder. In certain embodiments, for prophylactic benefit, the compositions are administered to a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
[0078] A“therapeutic effect,” as that term is used herein, encompasses a
therapeutic benefit and/or a prophylactic benefit as described above. A prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
[0079] The terms“co-administration,”“administered in combination with,” and their grammatical equivalents, as used herein, encompass administration of two or more agents to a subject, such as an animal, including humans, to treat a disease, disorder or condition described herein. In some embodiments, administration of the two or more agents is such that both agents and/or their metabolites are present in the subject at the same time. Co-administration includes simultaneous administration in separate compositions, administration at different times in separate compositions, or
administration in a composition in which the two or more agents are present.
[0080] An“anti-cancer agent,”“anti-tumor agent” or“chemotherapeutic agent” refers to any agent useful in the treatment of a neoplastic condition. One class of anti- cancer agents comprises chemotherapeutic agents.“Chemotherapy” means the administration of one or more chemotherapeutic drugs and/or other agents to a cancer patient by various methods, including intravenous, oral, intramuscular, intraperitoneal, intravesical, subcutaneous, transdermal, buccal, or inhalation or in the form of a suppository.
[0081] “Subject” refers to an animal, such as a mammal, for example, a human. The methods described herein can be useful in both human therapeutics and veterinary applications. In some embodiments, the subject is a mammal, and in some
embodiments, the subject is human.
[0082] “Mammal” includes humans and both domestic animals such as laboratory animals and household pets (e.g., cats, dogs, swine, cattle, sheep, goats, horses, rabbits), and non-domestic animals, such as wildlife and the like. In some embodiments, the mammal is a human.
[0083] “Radiation therapy” means exposing a subject, using routine methods and compositions known to the practitioner, to radiation emitters such as alpha-particle emitting radionuclides (e.g., actinium and thorium radionuclides), low linear energy transfer (LET) radiation emitters (i.e., beta emitters), conversion electron emitters (e.g., strontium-89 and samarium-153-EDTMP, or high-energy radiation, including without limitation x-rays, gamma rays, and neutrons.
[0084] The term“in vivo” refers to an event that takes place in a subject’s body.
[0085] Embodiments of the invention disclosed herein are also meant to encompass crystallin forms and/or polymorphs of a compound of structure (I), or a tautomer or zwitterioninc form thereof, being isotopically-labelled by having one or more atoms replaced by an atom having a different atomic mass or mass number (i.e., an“isotopic form” of the crystalline forms and/or polymorphs of a compound of structure (I), or a tautomer or zwitterionic form thereof). Examples of isotopes that can be incorporated into the disclosed crystalline forms and/or polymorphs, or a tautomer or zwitterionic form thereof, include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as 2H, 3H, 11C, 13C, 14C, 13N, 15N, 15O, 17O, 18O, 31P, 32P, 35S, 18F, 36Cl, 123I, and 125I, respectively. These radiolabeled compounds could be useful to help determine or measure the effectiveness of the compounds, by
characterizing, for example, the site or mode of action, or binding affinity to
pharmacologically important site of action. Certain isotopically-labeled crystalline forms and/or polymorphs of compounds of structure (I), or a tautomer or zwitterionic form thereof, for example, those incorporating a radioactive isotope, are useful in drug and/or substrate tissue distribution studies. The radioactive isotopes tritium (i.e., 3H), and carbon-14 (i.e., 14C) are particularly useful for this purpose in view of their ease of incorporation and ready means of detection.
[0086] Substitution with heavier isotopes such as deuterium (i.e., 2H) may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage requirements, and hence are preferred in some circumstances.
[0087] Substitution with positron emitting isotopes, such as 11C, 18F, 15O and 13N, can be useful in positron emission topography (PET) studies for examining substrate receptor occupancy. Isotopically-labeled crystalline forms and/or polymorphs of compounds of structure (I), or a tautomer or zwitterionic form thereof, can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described in the Examples as set out below using an appropriate isotopically-labeled reagent in place of the non-labeled reagent previously employed.
[0088] It is understood that in the present description, combinations of substituents and/or variables of the depicted formulae are permissible only if such contributions result in stable compounds.“Stable compound” and“stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
[0089] A“pharmaceutical composition” refers to a formulation of a compound of the disclosure and a medium generally accepted in the art for the delivery of the biologically active compound to mammals, e.g., humans. Such a medium includes all pharmaceutically acceptable carriers, diluents or excipients therefor.
[0090] "Pharmaceutically acceptable carrier or excipient" includes without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye/colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier which has been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.
[0091] “Pharmaceutically acceptable salt” includes both acid and base addition salts. [0092] “Pharmaceutically acceptable acid addition salt” refers to those salts which retain the biological effectiveness and properties of the free bases, which are not biologically or otherwise undesirable, and which are formed with inorganic acids such as, but are not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as, but not limited to, acetic acid, 2,2-dichloroacetic acid, adipic acid, alginic acid, ascorbic acid, aspartic acid, benzenesulfonic acid, benzoic acid, 4-acetamidobenzoic acid, camphoric acid, camphor-10-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecylsulfuric acid, ethane-1,2-disulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, formic acid, fumaric acid, galactaric acid, gentisic acid, glucoheptonic acid, gluconic acid, glucuronic acid, glutamic acid, glutaric acid, 2-oxo-glutaric acid, glycerophosphoric acid, glycolic acid, hippuric acid, isobutyric acid, lactic acid, lactobionic acid, lauric acid, maleic acid, malic acid, malonic acid, mandelic acid, methanesulfonic acid, mucic acid,
naphthalene-1,5-disulfonic acid, naphthalene-2-sulfonic acid, 1-hydroxy-2-naphthoic acid, nicotinic acid, oleic acid, orotic acid, oxalic acid, palmitic acid, pamoic acid, propionic acid, pyroglutamic acid, pyruvic acid, salicylic acid, 4-aminosalicylic acid, sebacic acid, stearic acid, succinic acid, tartaric acid, thiocyanic acid, p-toluenesulfonic acid, trifluoroacetic acid, undecylenic acid, and the like.
[0093] “Pharmaceutically acceptable base addition salt” refers to those salts which retain the biological effectiveness and properties of the free acids, which are not biologically or otherwise undesirable. These salts are prepared from addition of an inorganic base or an organic base to the free acid. Salts derived from inorganic bases include, but are not limited to, the sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Preferred inorganic salts are the ammonium, sodium, potassium, calcium, and magnesium salts. Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as ammonia, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, diethanolamine, ethanolamine, deanol, 2-dimethylaminoethanol,
2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, benethamine, benzathine, ethylenediamine, glucosamine, methylglucamine, theobromine, triethanolamine, tromethamine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins and the like. Particularly preferred organic bases are isopropylamine, diethylamine, ethanolamine,
trimethylamine, dicyclohexylamine, choline and caffeine.
[0094] A“tautomer” refers to a proton shift from one atom of a molecule to another atom of the same molecule. Embodiments thus include tautomers of the disclosed compounds, crystalline forms and polymorphs.
[0095] “Zwitterionic form” refers to a form of a compound, wherein at least one functional group has a positive electrical charge, at least one functional group has a negative electrical charge, and the net charge of the entire molecule is zero. For example, the phosphate group (-PO3H2) of a compound having structure (I) may exist in an anionic form (e.g., -PO3H-), and the nitrogen atom of a compound having structure (I) may exist in the protonated (cationic) form. The compound having structure (II) is a zwitterionic form of the compound having structure (I), for example. Embodiments include zwitterions of the disclosed compounds, crystalline forms and polymorphs.
[0096] The chemical naming protocol and structure diagrams used herein are a modified form of the I.U.P.A.C. nomenclature system, using the ACD/Name Version 9.07 software program and/or ChemDraw Ultra Version 11.0.1 software naming program (CambridgeSoft). For complex chemical names employed herein, a substituent group is typically named before the group to which it attaches. For example, cyclopropylethyl comprises an ethyl backbone with a cyclopropyl substituent. Except as described below, all bonds are identified in the chemical structure diagrams herein, except for all bonds on some carbon atoms, which are assumed to be bonded to sufficient hydrogen atoms to complete the valency. Crystalline and Polymorph Forms of Compounds of Structure (I)
[0097] It has been found that compounds having structure (I), or a tautomer or zwitterionic form thereof, can exist in various crystalline and/or polymorphic forms.
[0098] Accordingly, one embodiment provides a crystalline form of a compound having the following structure (I):
Figure imgf000021_0002
or a tautomer or zwitterionic form thereof. In some embodiments, the crystalline form comprises Form B. In some embodiments, the crystalline form consists essentially of Form B. In some embodiments, the crystalline form consists of Form B. In some embodiments, the crystalline form (e.g., Form B) is substantially pure (e.g., of other physical forms of the compound having structure (I), or a tautomer or zwitterionic form thereof; of impurities; of alvocidib). In some embodiments, the crystalline form is of a compound having structure (II).
[0099] Form B has structure (II):
Figure imgf000021_0001
and is characterized, in some embodiments, by an x-ray powder diffraction (XRPD) pattern comprising at least three peaks (e.g., three peaks, at least four peaks, four peaks, at least five peaks, five peaks, six peaks) at 2-theta angles selected from the group consisting of 4.8 ± 0.2°, 10.8 ± 0.2°, 13.7 ± 0.2°, 14.9 ± 0.2°, 20.0 ± 0.2° and 24.6 ± 0.2°. In some embodiments, Form B is characterized by an XRPD pattern comprising peaks at the following 2-theta angles: 10.8 ± 0.2°, 14.9 ± 0.2° and 20.0 ± 0.2°. In some embodiments, Form B is characterized by an XRPD pattern comprising peaks at the following 2-theta angles: 4.8 ± 0.2°, 10.8 ± 0.2°, 14.9 ± 0.2° and 20.0 ± 0.2°. In some embodiments, Form B is characterized by an XRPD pattern comprising peaks at the following 2-theta angles: 4.8 ± 0.2°, 10.8 ± 0.2°, 13.7 ± 0.2°, 14.9 ± 0.2° and 20.0 ± 0.2°. In some embodiments, Form B has an XRPD pattern substantially in accordance with that depicted in FIG.1. In some embodiments, Form B is characterized by a DSC thermogram comprising an endothermic peak at about 264 °C. In some embodiments, Form B is characterized by a DSC thermogram substantially in accordance with that depicted in FIG.8.
[00100] One embodiment provides a polymorph of a compound having the following structure (I):
Figure imgf000022_0001
or a tautomer or zwitterionic form thereof, the polymorph having an X-ray powder diffraction pattern comprising the following:
Figure imgf000022_0002
expressed in terms of "D" spacing.
[00101] In a related embodiment, the polymorph has an X-ray powder diffraction pattern comprising the following:
Figure imgf000022_0003
expressed in terms of "D" spacing. [00102] In yet another related embodiment, the polymorph has an X-ray powder diffraction pattern comprising the following:
Figure imgf000023_0001
expressed in terms of "D" spacing.
[00103] One embodiment provides a polymorph of a compound of structure (I), or a tautomer or zwitterion thereof, wherein the polymorph is a crystalized form having a monoclinic space group P21 with lattice parameters of:
Figure imgf000023_0002
and a volume of 1066.11(4) Å3.
[00104] Another embodiment provides a polymorph of a compound of structure (I), or a tautomer or zwitterion thereof, wherein the polymorph is a crystalized form having a monoclinic space group P21 with lattice parameters of:
Figure imgf000023_0003
and a volume of 1066.11(4) Å3.
[00105] Yet another embodiment provides a polymorph of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has the X-ray diffraction pattern set forth in FIG.1 (or substantially similar). In some embodiments, the polymorph has the X-ray diffraction pattern substantially similar to Table 6. [00106] Another related embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph is Form B.
[00107] One embodiment provides a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof wherein the polymorph is formed by a method comprising: a) contacting an amorphous compound of structure (I) with a lattice forming reagent; and
b) treating the product of step a) with solvent having water content less than about 0.05 % v/v and removing the solvent, thereby forming the polymorph.
[00108] In some more specific embodiments, the lattice forming reagent is maleic acid. In some embodiments, the solvent is ethanol or tetrahydrofuran. In some other embodiments, the contacting further comprises suspending the amorphous compound of structure (I) in aqueous tetrahydrofuran.
[00109] Another embodiment affords a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days above a temperature of about 22°C.
[00110] In certain related embodiments, the subsequent purity is at least 99.5% after being stored greater than about 7 days above a temperature of about 22°C. In some more specific embodiments, the subsequent purity is at least 99.5% after being stored greater than about 30 days above a temperature of about 20°C. In some embodiments, the initial purity and subsequent purity are as determined by HPLC.
[00111] Without wishing to be bound by theory, it is thought that the water content of the polymorph can have a significant effect on the purity and storage stability of the polymorph. That is, the polymorph can undergo a hydrolysis reaction that converts that phosphate moiety to a hydroxyl group. As such, an impurity may be present in the form of hydrolyzed structure (I) (i.e., alvocidib). However, it was unexpectedly discovered that keeping the water content of the polymorph and any subsequently formed compositions provided an active substance (i.e., the polymorph of structure (I)) with much more robust stability. [00112] Accordingly, some embodiments provide a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days above a temperature at about 25°C ± 2°C at a relative humidity of 60%. In some embodiments, the subsequent purity is at least 99.5% after being stored for greater than about 7 days at about 25°C ± 2°C at a relative humidity of 60%. In other embodiments, the subsequent purity is at least 99.5% after being stored for greater than about 30 days at about 25°C ± 2°C at a relative humidity of 60%. In some of the foregoing embodiments, the initial purity and subsequent purity are as determined by HPLC.
[00113] Still other embodiments provide a polymorph of a compound of structure (I) or a tautomer or zwitterionic form thereof, wherein the polymorph has an endotherm peak value at about 256.0°C– 268.0 (i.e., 262.0°C ± 6.0) as determined by differential scanning calorimetry. In some embodiments, the endotherm peak value is at a temperature ranging from 256°C to 268°C, from 257.0°C to 266.0°C or from 258.0°C to 265.0°C. In some more specific embodiments, the endotherm peak value is at about 259.0°C– 265.0°C.
[00114] In some embodiments of the foregoing, the polymorph comprises a zwitterionic form having the following structure (II):
Figure imgf000025_0001
[00115] In some of the foregoing embodiments, the polymorph has water content less than 0.50 % as determined by Karl Fischer titration. For example in some embodiments, the polymorph has water content less than 0.45 %, less than 0.40 %, less than 0.35 %, less than 0.30 %, less than 0.25 %, less than 0.20 %, less than 0.15 %, or less than 0.10 % as determined by Karl Fischer titration. Preparation of Compounds Having Structure (I)
[00116] It will be appreciated by those skilled in the art that the processes and reactions for preparing the compounds described herein may be modified in accordance with standard techniques to include alternative reagents and/or reaction conditions. For example, a reaction including an acid as lattice forming reagent may alternatively employ another suitable reagent such as a base, a sugar derivative, a peptide or other reagent.
[00117] One embodiment provides a method for preparing a polymorph, the method comprising: a) contacting an amorphous compound having the following structure (I):
Figure imgf000026_0001
with a lattice forming reagent; and
b) treating the product of step a) with solvent having water content less than about 0.05 % v/v; and removing the solvent, thereby forming the polymorph.
[00118] In some embodiments, the lattice forming reagent is an acid. For example, in some embodiments, the acid is an organic acid. In some embodiments the acid is an acid having a pKa greater than 1.0. In some embodiments the acid is a diprotic acid. In some specific embodiments, the acid is selected from the group consisting of maleic acid, fumaric acid, L-tartaric acid, hippuric acid, nicotinic acid, acetic acid, and combinations thereof. In some more specific embodiments, the lattice forming reagent is maleic acid.
[00119] In some specific embodiments, the contacting comprises adding the lattice forming reagent (e.g., maleic acid) in a 1:1 ± 0.5 ratio (e.g., molar ratio) of the amorphous compound of structure (I) to maleic acid. In more specific embodiments the ratio (e.g., molar ratio) is 1:1 ± 0.3, 1:1 ± 0.2, or 1:1 ± 0.1 compound of structure (I) to maleic acid. In other embodiments, the ratio (e.g., molar ratio) is from about 1:0.1 to about 1:10 (e.g., from about 1:0.1 to about 1:5) compound of structure (I) to maleic acid.
[00120] The lattice forming reagent is not limited to acids and can be any other compound that can be mixed with a compound of structure (I) and forms polymorph Form B. In particular, in some embodiments, the lattice forming reagent is a sugar or a peptide. In more specific embodiments, the lattice forming reagent is D-xylose. In other specific embodiments, the lattice forming reagent is aspartame.
[00121] The removing step is performed to remove residual solvent and lattice forming reagent and afford a solid product as a free base. Accordingly, in some embodiments the removing may involve reduced pressure (e.g., below 1 atm), a flow of air or inter gas (e.g., N2), increased temperature (e.g., above 25°C) or combinations thereof. In specific embodiments, the removing is at a pressure less than about 1 atm and a temperature greater than about 35°C. In some more specific embodiments, the pressure is less than about 0.9 atm, about 0.8 atm, about 0.7 atm, about 0.6 atm, or about 0.5 atm. In some embodiments, the temperature is above about 36 °C, about 37 °C, about 38 °C, about 39 °C, about 40 °C, about 42 °C, or about 45 °C. In some embodiments, the temperature is above the boiling point of residual solvent, e.g., about 100 °C. Each of the temperature and pressure values recited above include a range of ± 5% of the recited value (i.e., about 45°C includes 45°C ± 2.25°C).
[00122] In some embodiments, the removing comprises filtering the solid product away from residual solvent and/or lattice forming reagent.
[00123] Additionally, some embodiments of the methods recited above further comprise preparing a compound of structure (III):
Figure imgf000027_0001
by reacting a compound having the following structure:
Figure imgf000028_0001
or a salt thereof, with a base and a compound having the following structure:
Figure imgf000028_0002
[00124] In some of the foregoing embodiments, the base is an amine base, (e.g., triethylamine, diisopropylethyl amine). In some of the foregoing embodiments, amine base is added in an organic solvent.
[00125] In some embodiments, the method further comprises preparing the amorphous compound of structure (I):
Figure imgf000028_0003
by reacting a compound of structure (III), or a salt thereof, with a phosphoester cleaving compound and treating with a basic solution.
[00126] In some embodiments, the phosphoester cleaving compound is an organosilicon (e.g., trimethyl silyl bromide,“TMSBr”). In some embodiments, the basic solution comprises ammonium (e.g., ammonium bicarbonate). In some embodiments, the basic solution comprises acetonitrile. In some embodiments, the basic solution comprises aqueous acetonitrile.
[00127] In some embodiments, the polymorph is a polymorph as described in the foregoing embodiments. Additionally, one embodiment provides a polymorph that is prepared according to any of the methods described herein. [00128] Thus, in any of the embodiments described herein involving polymorph conversion/formation (e.g., preparation of crystalline Form B of a compound having structure (II)), the polymorph conversion/formation step(s) comprise crystallizing compound having structure (I) (e.g., amorphous compound having structure (I)), or a tautomer or zwitterionic form thereof, from an acidic solution (e.g., having a pH of greater than about 1; having a pH of greater than about 1 to less than about 5, for example, from about 1 to about 4, from about 2 to about 5). In some embodiments, the acidic solution comprises a lattice forming reagent (e.g., an acid, such as maleic acid; an acid having a pKa of greater than about 1; an acid having at least one pKa of less than about 5 and a pKa of greater than about 1, for example, at least one pKa of less than about 4 and a pKa of greater than about 1, at least one pKa of less than about 5 and a pKa of greater than about 2) and a solvent.
[00129] One embodiment is a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting amorphous compound having structure (I), or a tautomer or zwitterionic form thereof, with a lattice forming reagent (e.g., an acid, such as maleic acid; an acid having a pKa of greater than about 1; an acid having at least one pKa of less than about 5 and a pKa of greater than about 1, for example, an acid having at least one pKa of less than about 4 and a pKa of greater than about 1, an acid having at least one pKa of less than about 5 and a pKa of greater than about 2) in a solvent, thereby preparing the crystalline Form B of the compound having structure (II).
[00130] One embodiment is a method for preparing crystalline Form B of a compound having structure (II), the method comprising contacting a compound having structure (V):
,
Figure imgf000029_0001
or a tautomer, salt or zwitterionic form thereof, with an acid in a solvent, thereby preparing the crystalline Form B of the compound having structure (II). In some embodiments, the molar ratio of acid to compound having structure (V), or a tautomer, salt or zwitterionic form thereof, is from about 0.1:1 to about 10:1 (e.g., from about 0.1:1 to about 5:1; from about 0.4:1 to about 1.1:1; about 0.5:1).
[00131] In one embodiment, the lattice forming reagent is an acid. In some embodiments, the acid for preparing crystalline Form B has at least one pKa value that is less than about 5 (e.g., less than about 4) and/or a pKa value of greater than about 1 (e.g., greater than about 2).
[00132] In some embodiments for preparing crystalline Form B, the acid is an organic acid. As used herein,“organic acid” is an organic compound with acidic properties. Typically, an organic acid contains at least one carboxyl group (-COOH). Organic acids include, but are not limited to, maleic acid, acetic acid, citric acid and propionic acid. In some embodiments, the organic acid is maleic acid.
[00133] As used herein,“solvent” refers to a liquid that serves as a medium for a chemical reaction or other procedure in which compounds are being manipulated (e.g., crystallization). Typically, the solvent in the methods disclosed herein is an organic solvent or water, or a combination thereof. Examples of organic solvents include polar, protic solvents (e.g., an alcohol such as methanol, ethanol, butanol), polar aprotic solvents (e.g., dimethylformamide, tetrahydrofuran, ethyl acetate, acetone, methyl ethyl ketone) or nonpolar solvents (e.g., diethyl ether). In some embodiments, the solvent comprises tetrahydrofuran. In some embodiments, the solvent is a mixture of methanol and acetone.
[00134] Also provided are methods for preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof (e.g., a compound having structure (II)). The method comprises contacting a compound having the following structure (IV):
Figure imgf000030_0001
or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof, and contacting the compound having structure (V), or a tautomer or salt thereof, with an acid (e.g., maleic acid), thereby preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof. In some embodiments, the method further comprises contacting di-tert-butylphosphonate with carbon tetrahalide (e.g., carbon tetrachloride, carbon tetrabromide) to prepare the di-tert-butylhalophosphonate (e.g., di- tert-butylchlorophosphonate, di-tert-butylbromophosphonate, respectively). In some embodiments, the di-tert-butylhalophosphonate is prepared in situ with the compound having structure (IV), or a salt thereof, by contacting di-tert-butylphosphonate with carbon tetrahalide (e.g., carbon tetrachloride, carbon tetrabromide). In some
embodiments, the acid is hydrochloric acid or acetic acid, or a combination thereof.
[00135] “Amine base,” as used herein, refers to a compound that contains a nitrogen atom with a lone pair.“Amine base” includes primary, secondary and tertiary amine bases, as well as ammonia. Typically, the amine base is an organic amine base.
Examples of organic amine bases include, but are not limited to, diisopropylethylamine, tert-butylamine and triethylamine.
[00136] It will be appreciated that when an acid having a pKa of less than about the pKa of the phosphate group (-PO2OH) of a compound having structure (I) (e.g., hydrochloric acid) is used in the methods described herein, a salt (e.g., a hydrochloride salt) of the compound having structure (I) will result. Thus, in some embodiments, the compound formed by contacting a compound having structure (V), or a tautomer or salt thereof, with an acid is a salt of a compound having structure (I). In such instances, in some embodiments, the method further comprises contacting the salt of the compound having structure (I) with a base (e.g., ammonium bicarbonate), thereby forming the compound having structure (I), or a tautomer or zwitterionic form thereof.
[00137] One embodiment is a method for preparing crystalline Form B of a compound having structure (II). The method comprises contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di- tert-butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof, in an organic solvent, with an acid having a pKa value of greater than about 1 (e.g., an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1, for example, at least one pKa value that is less than about 4 and a pKa value of greater than about 1, at least one pKa value that is less than about 5 and a pKa value of greater than about 2), thereby preparing crystalline Form B of a compound having structure (II).
[00138] Another embodiment is a method for preparing crystalline Form B of a compound having structure (II), comprising contacting a compound having structure (IV), or a tautomer or salt thereof, with di-tert-butylhalophosphonate (e.g., di-tert- butylchlorophosphonate, di-tert-butylbromophosphonate) in the presence of an amine base, thereby forming a compound having structure (V), or a tautomer or salt thereof; and contacting the compound having structure (V), or a tautomer or salt thereof (e.g., in an organic solvent) with an acid having a pKa value of less than about 1, thereby forming a salt of a compound having structure (I); contacting the salt of a compound having structure (I) with a base, thereby forming amorphous compound having structure (I); and contacting the amorphous compound having structure (I) with an acid having a pKa value of greater than about 1 (e.g., an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1, for example, at least one pKa value that is less than about 4 and a pKa value of greater than about 1, at least one pKa value that is less than about 5 and a pKa value of greater than about 2), thereby preparing crystalline Form B of a compound having structure (II).
[00139] It will also be appreciated by those skilled in the art that in the processes for preparing the compounds described herein, the functional groups of intermediate compounds may need to be protected by suitable protecting groups. Such functional groups include hydroxy, amino, mercapto and carboxylic acid. Suitable protecting groups for hydroxy include trialkylsilyl or diarylalkylsilyl (for example, t- butyldimethylsilyl, t-butyldiphenylsilyl or trimethylsilyl), tetrahydropyranyl, benzyl, and the like. Suitable protecting groups for amino, amidino and guanidino include t- butoxycarbonyl, benzyloxycarbonyl, and the like. Suitable protecting groups for mercapto include -C(O)-R" (where R" is alkyl, aryl or arylalkyl), p-methoxybenzyl, trityl and the like. Suitable protecting groups for carboxylic acid include alkyl, aryl or arylalkyl esters. Protecting groups are optionally added or removed in accordance with standard techniques, which are known to one skilled in the art and described herein. The use of protecting groups is described in detail in Green, T.W. and P.G.M. Wutz, Protective Groups in Organic Synthesis (1999), 3rd Ed., Wiley. As one of skill in the art would appreciate, the protecting group may also be a polymer resin such as a Wang resin, Rink resin or a 2-chlorotrityl-chloride resin.
[00140] The following General Reaction Scheme 1 illustrates an exemplary method of forming a polymorph of a compound of structure (I):
.
Figure imgf000033_0001
[00141] It is understood that one skilled in the art may be able to make these compounds by similar methods or by combining other methods known to one skilled in the art. It is also understood that one skilled in the art would be able to make, in a similar manner as described below, a compound of structure (I), or a tautomer, salt or zwitterionic form thereof, not specifically illustrated below by using the appropriate starting components and modifying the parameters of the synthesis as needed (e.g., reagents, solvents, reaction times and temperatures, etc.). In general, starting components may be obtained from sources such as Sigma Aldrich, Lancaster Synthesis, Inc., Maybridge, Matrix Scientific, TCI, and Fluorochem USA, etc. or synthesized according to sources known to those skilled in the art (see, for example, Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th edition (Wiley, December 2000)) or prepared as described in this invention.
[00142] Polymorphs and compounds were analyzed using techniques known in the art, for example, by x-ray powder diffraction (XRPD), dynamic vapor sorption (DVS), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), mass spectrometry, high performance (or pressure) liquid chromatography (HPLC), 13C NMR, 31P NMR and/or 1H NMR. Synthetic procedures are described in more detail below.
Figure imgf000034_0001
[00143] Embodiments of the polymorph of a compound of structure (I) as shown can be prepared according to General Reaction Scheme 1. Certain intermediates useful for preparation of the compound having structure (I), or a tautomer, salt or zwitterionic form thereof (e.g., A-1, A-2, A-3, A-4, A-10, A-11) can be prepared according to methods described in U.S. Pat. No.9,758,539 and U.S. Pub. No.2007/0015802, which are incorporated herein by reference in their entireties. As shown in the General Reaction Scheme 1, A-1 can be purchased from commercial sources or prepared according to methods familiar to one of ordinary skill in the art. Reaction of A-1 with a strong Lewis acid (e.g., boron tribromide) affords A-2, which can then be
phosphorylated with an activated protected phosphate reagent (e.g., diethyl
chlorophosphate) under basic conditions (e.g., using diisopropyl ethyl amine as a base) in an appropriate solvent (e.g., NMP). The phosphorylated product (A-3) can then be deprotected under standard conditions (e.g., TMS-Br) and neutralized using suitable conditions (e.g., ammonium carbon ate in aqueous acetonitrile). The resultant compound A-4 (i.e., an amorphous solid or“Form A”) which is then converted to the polymorph A-5 using an appropriate lattice forming reagent (e.g., maleic acid) and a suitable solvent system (e.g., THF and water at 19:1 v/v). Finally, the lattice forming reagent is removed using a suitable, substantially anhydrous solvent (e.g., an alcohol such as ethanol) and dried to afford polymorph Form B.
[00144] It should be noted that the General Reaction Scheme 1 only depicts an exemplary method for preparation of the polymorph A-5 and other methods are available, using different reagents, and/or different intermediates, etc.
[00145] For example, General Reaction Scheme 2 describes another method for preparing Form A and Form B.
Figure imgf000035_0001
[00146] Reaction of A-1 with a strong Lewis acid (e.g., boron tribromide) affords A- 2, which can then be phosphorylated with an activated protected phosphate reagent (e.g., di-tert-butylhalophosphonate, such as di-tert-butylchlorophosphonate or di-tert- butylbromophosphonate) under basic conditions (e.g., using diisopropylethylamine as a base) in an appropriate solvent (e.g., dimethylformamide; DMF). In some
embodiments employing di-tert-butylhalophosphonate, the di-tert- butylhalophosphonate can be prepared (e.g., in situ with A-2) by contacting di-tert- butylphosphonate with carbon tetrahalide (e.g., carbon tetrachloride, carbon
tetrabromide). The phosphorylated product (A-10) can then be deprotected under acidic conditions (e.g., using hydrochloric and acetic acids). The resulting hydrochloride salt can then be converted to its free base and/or zwitterionic form, Form A (A-4), under neutralizing conditions (e.g., ammonium carbonate in aqueous acetonitrile). The resultant compound A-4 can then be converted to Form B (A-5) using an appropriate lattice forming reagent (e.g., an acid, such as maleic acid, acetic acid, citric acid, propionic acid) and a suitable solvent (e.g., THF and water at 19:1 v/v, methanol, methanol and aceton at 1:1 v/v). In some embodiments, the lattice forming reagent is removed from A-5 using a suitable, substantially anhydrous solvent (e.g., an alcohol such as ethanol), and resulting A-5 is dried to afford Form B.
[00147] General Reaction Scheme 3 provides yet another method for preparing Form B. General Reaction Scheme 3
Figure imgf000036_0001
[00148] As an alternative to performing the deprotection, free base/zwitterion formation and polymorph conversion steps in three, separate steps, some embodiments provide for deprotection and polymorph formation in a single step. Briefly, A-10 can be deprotected and converted to Form B (A-5) under acidic conditions (e.g., maleic acid in methanol and acetone at 1:1 v/v) to afford Form B. Pharmaceutical Compositions
[00149] In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof, is formulated into a pharmaceutical composition. In any of the pharmaceutical compositions described herein, the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof can be the compound having structure (II), or any crystalline form or polymorph of a compound of structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof described herein, e.g., Form B. [00150] A pharmaceutical composition, as used herein, refers to a mixture of the compound having structure (I) (e.g. a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, with other chemical components, such as carriers, stabilizers, diluents, dispersing agents, suspending agents, thickening agents, and/or excipients.
[00151] In particular, one embodiment provides a pharmaceutical composition comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof, and a pharmaceutically acceptable carrier or excipient.
[00152] In some embodiments, the pharmaceutical composition is formulated for oral administration. Pharmaceutical compositions described herein are formulated by combining the active (e.g., crystalline form and/or polymorph of a compound having structure (I), or a tautomer or zwitterionic form thereof) with, e.g., pharmaceutically acceptable carriers or excipients. In various embodiments, the crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof is formulated in an oral dosage form that includes, by way of example only, tablets, powders, pills, dragees, capsules, liquids, gels, syrups, elixirs, slurries, suspensions and the like. In some embodiments, the pharmaceutical composition comprises an oral capsule.
[00153] In some embodiments, the pharmaceutical composition comprises the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form), in a concentration ranging from about 0.5 weight percent to about 11.25 weight percent. In other specific embodiments, the pharmaceutical composition comprises the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form) in a concentration ranging from about 0.6 weight percent to about 11.05 weight percent.
[00154] In more specific embodiments, the pharmaceutical composition comprises about 0.6 weight percent of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In other specific embodiments, the pharmaceutical composition comprises about 2.5 weight percent of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In still other specific embodiments, the pharmaceutical composition comprises about 11.0 weight percent of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form).
[00155] In some more specific embodiments, the pharmaceutical composition comprises about 1 milligram (mg) of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In other specific embodiments, the pharmaceutical composition comprises about 4 mg of the compound having structure (I), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form). In some embodiments, the pharmaceutical composition comprises about 16 mg of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., in crystalline or polymorph form).
[00156] In embodiments, the excipient is anhydrous. In some embodiments, the excipient is anhydrous lactose or microcrystalline cellulose. In more specific embodiments, the excipient is anhydrous lactose. In some embodiments, the excipient is microcrystalline cellulose. In specific embodiments, the excipient is anhydrous microcrystalline cellulose.
[00157] In other embodiments, the excipient is anhydrous lactose or cornstarch (e.g., cornstarch).
[00158] In some of the foregoing embodiments, the pharmaceutical composition comprises the excipient in a concentration ranging from about 85 weight percent to about 98 weight percent. In more specific embodiments, the pharmaceutical composition comprises the excipient in a concentration ranging from about 87 weight percent to about 97.5 weight percent. In some embodiments, the pharmaceutical composition comprises about 87 weight percent of the excipient. In other
embodiments, the pharmaceutical composition comprises about 95.5 weight percent of the excipient.
[00159] In related embodiments, the pharmaceutical composition further comprises a glidant. In some embodiments, the glidant is colloidal silicon dioxide. In some of these embodiments, the pharmaceutical composition comprises about 1 weight percent of the glidant (e.g., colloidal silicon dioxide).
[00160] In some related embodiments, the pharmaceutical composition further comprises a lubricant. In some embodiments, the lubricant is magnesium stearate. In some of these embodiments, the pharmaceutical composition comprises about 1 weight percent of the lubricant (e.g., magnesium stearate). Other examples of lubricants are described in Example 13 herein.
[00161] In some related embodiments, the pharmaceutical composition further comprises a disintegrant. In some embodiments, the disintegrant is partly
pregelatinized starch, low-substituted hydroxyl propyl cellulose or carmellose calcium. Other examples of disintegrants are described in Example 13 herein.
[00162] One embodiment is a pharmaceutical composition comprising from about 0.5 weight percent to about 11.25 weight percent (e.g., from about 0.5 weight percent to about 1 weight percent, from about 10.5 weight percent to about 11.25 weight percent) of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), and from about 85 weight percent to about 99.5 weight percent (e.g., from about 95 weight percent to about 99.5 weight percent, from about 85 weight percent to about 90 weight percent, respectively) of a pharmaceutically acceptable carrier or excipient.
[00163] One embodiment is a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), about 97.4 weight percent of anhydrous lactose, about 1 weight percent colloidal silicon dioxide, and about 1 weight percent magnesium stearate. In a specific aspect of this embodiment, the pharmaceutical composition comprises about 1 mg of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)).
[00164] One embodiment is a pharmaceutical composition comprising about 11 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), about 87 weight percent of anhydrous lactose, about 1 weight percent colloidal silicon dioxide, and about 1 weight percent magnesium stearate. In a specific aspect of this embodiment, the pharmaceutical composition comprises about 16 mg of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)).
[00165] One embodiment is a pharmaceutical composition comprising about 0.6 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), and from about 98 weight percent to about 99.5 weight percent of cornstarch. In a specific aspect of this embodiment, the pharmaceutical composition further comprises about 1 weight percent magnesium stearate.
[00166] One embodiment is a pharmaceutical composition comprising about 11 weight percent of a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof (e.g., a compound having structure (II)), and about 88 weight percent of cornstarch. In a specific aspect of this embodiment, the pharmaceutical composition further comprises about 1 weight percent magnesium stearate.
[00167] In some of the foregoing embodiments, the pharmaceutical compositions are in the form of a capsule for oral administration.
[00168] In embodiments, a pharmaceutical composition described herein (e.g., comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof) is provided in the form of a rapid release formulation. As used herein,“rapid release formulation” refers to a formulation that does not delay or prolong release of an active contained therein. Typically, rapid release formulations release at least 70% of the active contained therein within 1 hour. In some embodiments, a rapid release formulation releases at least 75% of an active contained therein (e.g., a compound having structure (I), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof) within about 45 minutes. “Rapid release formulation” is also referred to as“immediate release formulation.”
[00169] In embodiments, a pharmaceutical composition described herein (e.g., comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof) is provided in the form of an extended release formulation. As used herein,“extended release formulation” refers to a formulation that releases an active contained therein in a controlled manner during an extended period of time, at a predetermined rate, duration, and location following administration.
[00170] In embodiments, a pharmaceutical composition described herein (e.g., comprising a crystalline form and/or polymorph of a compound of structure (I), or a tautomer or zwitterionic form thereof) is provided in the form of an intermediate release formulation. As used herein,“intermediate release formulation” refers to a formulation that delays or extends release of an active contained therein, or alters its site of release, but is not an extended release formulation, as that term is described herein.
[00171] The pharmaceutical composition may also be formulated for a route of administration other than oral. Other suitable routes of administration include intravenous, rectal, aerosol, parenteral, ophthalmic, pulmonary, transmucosal, transdermal, vaginal, otic, nasal, and topical administration. In addition, by way of example only, parenteral delivery includes intramuscular, subcutaneous, intravenous, intramedullary injections, as well as intrathecal, direct intraventricular, intraperitoneal, intralymphatic, and intranasal injections.
[00172] In certain embodiments, a pharmaceutical composition described herein is administered in a local rather than systemic manner, for example, via injection of the pharmaceutical composition directly into an organ, often in a depot preparation or sustained release formulation. In specific embodiments, long-acting formulations are administered by implantation (for example, subcutaneously or intramuscularly) or by intramuscular injection. Furthermore, in other embodiments, the pharmaceutical composition is delivered in the form of a targeted drug delivery system, for example, a liposome coated with organ-specific antibody. In such embodiments, the liposomes are targeted to and taken up selectively by the organ. In yet other embodiments, the pharmaceutical composition is provided in the form of a rapid release formulation, in the form of an extended release formulation, or in the form of an intermediate release formulation. In yet other embodiments, the pharmaceutical composition is administered topically.
[00173] In other embodiments, the pharmaceutical composition is formulated for transmucosal administration. In specific embodiments, transmucosal formulations include penetrants that are appropriate to the barrier to be permeated. In still other embodiments, wherein the pharmaceutical composition is formulated for other parenteral injections; appropriate formulations include aqueous or non-aqueous solutions. In specific embodiments, such solutions include physiologically compatible buffers and/or excipients.
[00174] In other embodiments, pharmaceutical compositions described herein are formulated for buccal or sublingual administration. Formulations suitable for buccal or sublingual administration include, by way of example only, tablets, lozenges, or gels.
[00175] In still other embodiments, the pharmaceutical composition described herein is formulated for parental injection, including bolus injection or continuous infusion. In specific embodiments, formulations for injection are presented in unit dosage form (e.g., in ampoules) or in multi-dose containers. Preservatives are, optionally, added to the injection formulations. In still other embodiments, the pharmaceutical compositions are formulated in a form suitable for parenteral injection as sterile suspensions, solutions or emulsions in oily or aqueous vehicles. Parenteral injection formulations optionally contain formulatory agents such as suspending, stabilizing and/or dispersing agents. In additional embodiments, suspensions are prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles for use in the
pharmaceutical compositions described herein include, by way of example only, fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or
triglycerides, or liposomes. In certain specific embodiments, aqueous injection suspensions contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension contains suitable stabilizers or agents which increase the solubility of the active to allow for the preparation of highly concentrated solutions. Alternatively, in other
embodiments, the active ingredient is in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
[00176] In some embodiments, the pharmaceutical composition is administered in dosages. It is known in the art that due to intersubject variability in compound pharmacokinetics, individualization of dosing regimen is necessary for optimal therapy. Dosing for the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, may be found by routine experimentation in light of the instant disclosure. [00177] The compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, according to certain embodiments, is effective over a wide dosage range. For example, in the treatment of adult humans, dosages from 0.01 to 1000 mg, from 0.5 to 100 mg, from 1 to 50 mg per day, and from 5 to 40 mg per day are examples of dosages that are used in some embodiments. An exemplary dosage is 10 to 30 mg per day. In various embodiments, the dosage is 3, 6, 9, 12, 16, 21, 28, 32, 42, or 50 mg per day. In some embodiments, the dosage ranges from about 1 mg to about 30 mg per day, e.g., about 1 mg, about 2 mg, about 4 mg, about 8 mg, about 12 mg, about 16 mg or about 22 mg per day. The exact dosage will depend upon the route of administration, the form in which the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered, the subject to be treated, the body weight of the subject to be treated, and the preference and experience of the attending physician.
[00178] In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof, is administered in a single dose. Routes of administration are selected and used as appropriate. A single dose of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, may also be used for treatment of an acute condition.
[00179] In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof, is administered in multiple doses. In some embodiments, dosing is about once, twice, three times, four times, five times, six times, or more than six times per day (e.g., twice per day). In other embodiments, dosing is about once a month, once every two weeks, once a week, or once every other day.
[00180] In another embodiment, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered about once per day to about 6 times per day. In another embodiment, the administration of the polymorph of a compound of structure (I) continues for less than about 7 days. In yet another embodiment, the administration continues for more than about 6, 10, 14, 28 days, two months, six months, or one year. In some cases, continuous dosing is achieved and maintained as long as necessary.
[00181] Administration of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, may continue as long as necessary. In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered for more than 1, 2, 3, 4, 5, 6, 7, 14, or 28 days. In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered for less than 28, 14, 7, 6, 5, 4, 3, 2, or 1 day. In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered chronically on an ongoing basis, e.g., for the treatment of chronic effects. In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered once daily for the first 21 days out of a 28-day cycle. In some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof is administered twice daily for the first 21 days out of a 28-day cycle. A cycle may be repeated at least once, at least twice, at least three times, or at least four times.
[00182] In certain embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is administered as a pharmaceutical composition in which the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form, is mixed with one or more other active ingredients, as in combination therapy. Accordingly, in embodiments, provided is a pharmaceutical combination comprising a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, and one or more additional therapeutic agents (e.g., chemotherapeutic agents). Encompassed herein are all combinations of actives set forth in the combination therapies section below and throughout this disclosure.
[00183] In some of the foregoing embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, has a water content less than 0.50%, as determined by Karl Fischer titration. For example, in some embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, has a water content less than 0.45%, less than 0.40%, less than 0.35%, less than 0.30%, less than 0.25%, less than 0.20%, less than 0.15%, or less than 0.10%, as determined by Karl Fischer titration.
[00184] Some particular embodiments provide a unit dose form comprising a pharmaceutical composition as described herein. In various embodiments, the unit dose form is formulated for oral administration. In some embodiments, the unit dose form is a capsule. In some embodiments, the unit dose form is a tablet.
[00185] In some embodiments, dosage forms, such as dragee cores and tablets, are provided with one or more suitable coatings. In specific embodiments, concentrated sugar solutions are used for coating the dosage form. The sugar solutions, optionally contain additional components, such as, by way of example only, gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs and/or pigments are also optionally added to the coatings for identification purposes.
Additionally, the dyestuffs and/or pigments are optionally utilized to characterize different combinations of active compound doses.
[00186] In some embodiments, the unit dose form comprises the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, in a concentration ranging from about 0.5 weight percent to about 11.25 weight percent. In other specific embodiments, the unit dose form comprises the polymorph in a concentration ranging from about 0.6 weight percent to about 11.05 weight percent. [00187] In more specific embodiments, the unit dose form comprises about 0.6 weight percent of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In other specific embodiments, the unit dose form comprises about 2.5 weight percent of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In still other specific embodiments, the unit dose form comprises about 11.0 weight percent of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
[00188] In some more specific embodiments, the unit dose form comprises about 1 milligram (mg) of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In other specific embodiments, the unit dose form comprises about 4 mg of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In some embodiments, the unit dose form comprises about 16 mg of the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof.
[00189] In some of the foregoing embodiments, the unit dose form comprises the excipient in a concentration ranging from about 85 weight percent to about 98 weight percent. In more specific embodiments, the unit dose form comprises the excipient in a concentration ranging from about 87 weight percent to about 97.5 weight percent. In some embodiments, the unit dose form comprises about 87 weight percent of the excipient. In other embodiments, the unit dose form comprises about 95.5 weight percent of the excipient.
[00190] In embodiments, the excipient is anhydrous. In some embodiments, the excipient is anhydrous lactose or microcrystalline cellulose. In more specific embodiments, the excipient is anhydrous lactose. In some embodiments, the excipient is microcrystalline cellulose. In specific embodiments, the excipient is anhydrous microcrystalline cellulose.
[00191] In some embodiments, the excipient is anhydrous lactose or cornstarch.
[00192] In related embodiments, the unit dose form further comprises a glidant. In some embodiments, the glidant is colloidal silicon dioxide. In some of these embodiments, the unit dose form comprises about 1 weight percent of the glidant (e.g., colloidal silicon dioxide).
[00193] In some related embodiments, the unit dose form further comprises a lubricant. In some embodiments, the lubricant is magnesium stearate. In some of these embodiments, the unit dose form comprises about 1 weight percent of the lubricant (e.g., magnesium stearate). Other examples of lubricants are described in Example 13 herein.
[00194] In some related embodiments, the pharmaceutical composition further comprises a disintegrant. In some embodiments, the disintegrant is partly
pregelatinized starch, low-substituted hydroxyl propyl cellulose or carmellose calcium. Other examples of disintegrants are described in Example 13 herein.
[00195] In particular embodiments, the unit dose form is in the form of a capsule for oral administration, e.g., a hydroxypropylmethylcellulose capsule. In certain embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, are formulated into other oral dosage forms. Oral dosage forms include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. In specific embodiments, push-fit capsules contain the active ingredients in admixture with one or more fillers. Fillers include, by way of example only, lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In other embodiments, soft capsules contain the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, dissolved or suspended in a suitable liquid. Suitable liquids include, by way of example only, one or more fatty oil, liquid paraffin, or liquid polyethylene glycol. In addition, stabilizers are optionally added. [00196] The pharmaceutical compositions described herein are formulated in any conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compound(s) into preparations which can be used pharmaceutically. In certain embodiments, the formulation of the pharmaceutical composition facilitates administration to a subject.
[00197] Proper formulation is dependent upon the route of administration chosen. Any pharmaceutically acceptable techniques, carriers, and excipients are optionally used as suitable to formulate the pharmaceutical compositions described herein:
Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington’s Pharmaceutical Sciences, Mack Publishing Co., Easton, Pennsylvania 1975; Liberman, H.A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins1999), the relevant teachings of which are incorporated herein by reference in their entireties.
[00198] In embodiments, pharmaceutical compositions described herein are manufactured in a conventional manner, such as, by way of example only, by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or compression processes.
[00199] In particular embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is mixed with an excipient and, optionally, a lubricant and a glidant using direct blending techniques, and capsules are filled with the resulting mixture on a manual capsule filling machine. In some particular embodiments, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof, the excipient and the optional glidant are put through a 500 µm screen, then mixed together, and blended for 16 minutes at 30 rpm. The optional lubricant is then sieved through a 250 µm screen and added to the mixture. The resulting mixture is then blended for 5 minutes at 30 rpm. Capsules are then filled using an overage of from 0% to about 5% (e.g., about 1%), using tamping and/or tapping, as needed. [00200] In certain embodiments, pharmaceutical preparations for oral use are obtained by mixing one or more solid excipients with the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as: for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others, such as polyvinylpyrrolidone (PVP or povidone) or calcium phosphate. In specific
embodiments, disintegrating agents are optionally added. Disintegrating agents include, by way of example only, cross-linked croscarmellose sodium, polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
[00201] Additionally, the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, can encompass unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as, for example, ethanol, and the like. The solvated forms of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, are also considered to be disclosed herein. In addition, the pharmaceutical compositions optionally include other medicinal or pharmaceutical agents, carriers, adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure, buffers, and/or other therapeutically valuable substances.
[00202] Methods for the preparation of compositions comprising the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, include formulating with one or more inert, pharmaceutically acceptable excipients or carriers to form a solid, semi-solid or liquid. Solid compositions include powders, tablets, dispersible granules, capsules, cachets, and suppositories. Liquid compositions include solutions in which the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is dissolved, emulsions comprising the compound having structure (I), or a tautomer,
pharmaceutically acceptable salt or zwitterionic form thereof, or a solution containing liposomes, micelles, or nanoparticles comprising the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. Semi-solid compositions include gels, suspensions and creams. The form of the pharmaceutical compositions described herein include liquid solutions or suspensions, solid forms suitable for solution or suspension in a liquid prior to use, or as emulsions. These compositions also optionally contain minor amounts of nontoxic, auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, and so forth.
[00203] In some embodiments, the pharmaceutical composition comprising the compound having structure (I) (e.g., a crystalline form and/or polymorph of a compound having structure (I)), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, takes the form of a liquid where the agents are present in solution, in suspension or both. Typically, when the composition is administered as a solution or suspension, a first portion of the agent is present in solution and a second portion of the agent is present in particulate form, in suspension in a liquid matrix. In some embodiments, a liquid composition includes a gel formulation. In other embodiments, the liquid composition is aqueous.
[00204] In certain embodiments, useful aqueous suspensions contain one or more polymers as suspending agents. Useful polymers include water-soluble polymers, such as cellulosic polymers, e.g., hydroxypropylmethylcellulose, and water-insoluble polymers, such as cross-linked carboxyl-containing polymers. Certain pharmaceutical compositions described herein comprise a mucoadhesive polymer, selected, for example, from carboxymethylcellulose, carbomer (acrylic acid polymer),
poly(methylmethacrylate), polyacrylamide, polycarbophil, acrylic acid/butyl acrylate copolymer, sodium alginate or dextran.
[00205] Useful pharmaceutical compositions also, optionally, include solubilizing agents to aid in the solubility of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. The term“solubilizing agent” generally includes agents that result in formation of a micellar solution or a true solution of the agent. Certain acceptable nonionic surfactants, for example, polysorbate 80, are useful as solubilizing agents, as are ophthalmically acceptable glycols, polyglycols, e.g., polyethylene glycol 400, and glycol ethers.
[00206] Furthermore, pharmaceutical compositions optionally include one or more pH adjusting agents or buffering agents, including acids, such as acetic, boric, citric, lactic, phosphoric and hydrochloric acids; bases such as sodium hydroxide, sodium phosphate, sodium borate, sodium citrate, sodium acetate, sodium lactate and tris- hydroxymethylaminomethane; and buffers such as citrate/dextrose, sodium bicarbonate and ammonium chloride. Such acids, bases and buffers are included in an amount required to maintain pH of the composition in an acceptable range.
[00207] Pharmaceutical compositions also, optionally, include one or more salts in an amount required to bring osmolality of the composition into an acceptable range. Such salts include those having, for example, sodium, potassium or ammonium cations and chloride, citrate, ascorbate, borate, phosphate, bicarbonate, sulfate, thiosulfate or bisulfite anions; suitable salts include sodium chloride, potassium chloride, sodium thiosulfate, sodium bisulfite and ammonium sulfate.
[00208] Pharmaceutical compositions optionally include one or more preservatives to inhibit microbial activity. Suitable preservatives include mercury-containing substances such as merfen and thiomersal; stabilized chlorine dioxide; and quaternary ammonium compounds such as benzalkonium chloride, cetyltrimethylammonium bromide and cetylpyridinium chloride.
[00209] Still other pharmaceutical compositions include one or more surfactants to enhance physical stability or for other purposes. Suitable nonionic surfactants include polyoxyethylene fatty acid glycerides and vegetable oils, e.g., polyoxyethylene (60) hydrogenated castor oil; and polyoxyethylene alkylethers and alkylphenyl ethers, e.g., octoxynol 10, octoxynol 40.
[00210] Still other pharmaceutical compositions include one or more antioxidants to enhance chemical stability where required. Suitable antioxidants include, by way of example only, ascorbic acid and sodium metabisulfite.
[00211] In certain embodiments, aqueous suspension compositions are packaged in single-dose non-reclosable containers. Alternatively, multiple-dose, reclosable containers are used, in which case it is typical to include a preservative in the composition. [00212] In alternative embodiments, other delivery systems for hydrophobic pharmaceutical compounds are employed. Liposomes and emulsions are examples of delivery vehicles or carriers useful herein. In certain embodiments, organic solvents such as N-methylpyrrolidone are also employed. In additional embodiments, the compounds described herein are delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the active. Various sustained-release materials are useful herein. In some embodiments, sustained-release capsules release the active for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the active, additional strategies for protein stabilization are employed.
[00213] In certain embodiments, the formulations described herein comprise one or more antioxidants, metal chelating agents, thiol-containing compounds and/or other general stabilizing agents. Examples of such stabilizing agents, include: (a) about 0.5% to about 2% w/v glycerol, (b) about 0.1% to about 1% w/v methionine, (c) about 0.1% to about 2% w/v monothioglycerol, (d) about 1 mM to about 10 mM EDTA, (e) about 0.01% to about 2% w/v ascorbic acid, (f) 0.003% to about 0.02% w/v polysorbate 80, (g) 0.001% to about 0.05% w/v. polysorbate 20, (h) arginine, (i) heparin, (j) dextran sulfate, (k) cyclodextrins, (l) pentosan polysulfate and other heparinoids, (m) divalent cations such as magnesium and zinc; or (n) combinations thereof.
[00214] In some embodiments, the concentration of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, provided in a pharmaceutical composition or unit dose form is no more than 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19%, 18%, 17%, 16%, 15%,14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002%, or 0.0001% w/w, w/v or v/v.
[00215] In some embodiments, the concentration of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is in the range of from approximately 0.0001% to approximately 50%, approximately 0.001% to approximately 40 %, approximately 0.01% to approximately 30%, approximately 0.02% to approximately 29%, approximately 0.03% to approximately 28%, approximately 0.04% to approximately 27%, approximately 0.05% to
approximately 26%, approximately 0.06% to approximately 25%, approximately 0.07% to approximately 24%, approximately 0.08% to approximately 23%, approximately 0.09% to approximately 22%, approximately 0.1% to approximately 21%,
approximately 0.2% to approximately 20%, approximately 0.3% to approximately 19%, approximately 0.4% to approximately 18%, approximately 0.5% to approximately 17%, approximately 0.6% to approximately 16%, approximately 0.7% to approximately 15%, approximately 0.8% to approximately 14%, approximately 0.9% to approximately 12%, or approximately 1% to approximately 10% w/w, w/v or v/v.
[00216] In some embodiments, the concentration of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, is in the range of from approximately 0.001% to approximately 10%, approximately 0.01% to approximately 5%, approximately 0.02% to approximately 4.5%, approximately 0.03% to approximately 4%, approximately 0.04% to approximately 3.5%,
approximately 0.05% to approximately 3%, approximately 0.06% to approximately 2.5%, approximately 0.07% to approximately 2%, approximately 0.08% to
approximately 1.5%, approximately 0.09% to approximately 1%, or approximately 0.1% to approximately 0.9% w/w, w/v or v/v.
[00217] In some embodiments, the amount of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, provided in a pharmaceutical composition or unit dose form is no more than 10 g, 9.5 g, 9.0 g, 8.5 g, 8.0 g, 7.5 g, 7.0 g, 6.5 g, 6.0 g, 5.5 g, 5.0 g, 4.5 g, 4.0 g, 3.5 g, 3.0 g, 2.5 g, 2.0 g, 1.5 g, 1.0 g, 0.95 g, 0.9 g, 0.85 g, 0.8 g, 0.75 g, 0.7 g, 0.65 g, 0.6 g, 0.55 g, 0.5 g, 0.45 g, 0.4 g, 0.35 g, 0.3 g, 0.25 g, 0.2 g, 0.15 g, 0.1 g, 0.09 g, 0.08 g, 0.07 g, 0.06 g, 0.05 g, 0.04 g, 0.03 g, 0.02 g, 0.01 g, 0.009 g, 0.008 g, 0.007 g, 0.006 g, 0.005 g, 0.004 g, 0.003 g, 0.002 g, 0.001 g, 0.0009 g, 0.0008 g, 0.0007 g, 0.0006 g, 0.0005 g, 0.0004 g, 0.0003 g, 0.0002 g, or 0.0001 g. Methods of Treatment
[00218] Embodiments of the present disclosure include methods for treating a disease associated with overexpression of a cyclin-dependent kinase (CDK), such as CDK 9, 1, 2, 4 or 7 (e.g., CDK9), in a mammal in need thereof, comprising
administering to the mammal a therapeutically effective amount of a compound having structure (I) (e.g., a crystalline form and/or polymorph thereof), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof; pharmaceutical composition; and/or unit dose form described herein. In some embodiments, the disease associated with overexpression of a CDK is cancer.
[00219] Some embodiments include methods for treatment of cancer comprising administering an effective amount of a compound having structure (I) (e.g., a crystalline form and/or polymorph thereof), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, to a subject in need thereof. Certain embodiments provide a method for treatment of cancer, the method comprising administering an effective amount of a pharmaceutical composition comprising a compound having structure (I) (e.g., a crystalline form and/or polymorph thereof), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, to a subject in need thereof. The compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, may be used singly or in combination with one or more therapeutic agents, for example, as components of one or more mixtures.
[00220] In some embodiments, the cancer treated is a hematologic cancer.
Hematologic malignancies that can be treated with a compound having structure (I), or a tautomer or zwitterionic form thereof, include leukemias and lymphomas. In some embodiments, the hematologic cancer is selected from acute myelogenous leukemia (AML), follicular lymphoma, acute lymphoblastic leukemia (ALL), chronic
lymphocytic leukemia (CLL), multiple myeloma (MM) and non-Hodgkin’s lymphoma (e.g., AML, follicular lymphoma, ALL, CLL and non-Hodgkin’s lymphoma). In more specific embodiments, the hematological cancer is AML. In other more specific embodiments, the hematologic cancer is CLL. In more specific embodiments, the hematologic cancer is MM. In still other specific embodiments, the hematologic cancer is myelodysplasic syndrome (MDS).
[00221] In other embodiments, the cancer comprises a solid tumor. Accordingly, in some embodiments, the cancer is a solid tumor cancer. In various embodiments, the solid tumor cancer is breast cancer, bladder cancer, liver cancer, pancreatic cancer, lung cancer, colorectal cancer, ovarian cancer, prostate cancer, or melanoma. In some embodiments, the cancer is bladder cancer. In some embodiments, the cancer is lung cancer. In other embodiments, the cancer is liver cancer. In some embodiments, the cancer is a sarcoma, bladder cancer or renal cancer. In some embodiments, the cancer is prostate cancer (e.g., castration-resistant prostate cancer, castration-sensitive prostate cancer). In other embodiments, the cancer is bladder cancer, pancreatic cancer, colorectal cancer, kidney cancer, non-small cell lung carcinoma, prostate cancer, sarcoma, skin cancer, thyroid cancer, testicular cancer or vulvar cancer. In some embodiments, the cancer is endometrial cancer, pancreatic cancer, testicular cancer, renal cancer, melanoma, colorectal cancer, thyroid cancer, bladder cancer, pancreatic cancer, vulvar cancer, sarcoma, prostate cancer, lung cancer or anal cancer. In some embodiments, the cancer is a sarcoma. In some embodiments, the cancer is a renal cell carcinoma.
[00222] “Castration-resistant prostate cancer” refers to prostate cancer that progresses in a subject following administration of one or more androgen depletion therapies (ADTs). Progression of prostate cancer can be evidenced by, for example, a prostate-specific antigen doubling time (PSADT) of less than or equal to 10 months, the progression of pre-existing disease (e.g., radiographic progression, clinical progression, a skeletal-related event, prostate-specific antigen (PSA) progression), and/or the appearance of new metastases in a subject, and is typically driven by androgens, which are a class of hormones including testosterone and dihydrotestosterone (DHT). These androgens bind to the androgen receptor (AR), which is a transcription activator that promotes growth and survival of prostate cells, including prostate cancer cells. ADT refers to a therapy to suppress androgen levels (e.g., surgical castration or chemical castration) or androgen signaling (e.g., by reducing androgen binding to androgen receptor), which may be used to slow the progression of prostate cancer. Androgen deprivation therapy typically causes a temporary reduction in tumor burden
concomitant with a decrease in serum PSA. Mechanisms of castration resistance include the emergence of AR variants that are active in the absence of androgen, including splice variants, point mutations to AR, and AR gene amplifications. Castration resistance can be biochemically characterized before the onset of symptoms by a rising titer of serum PSA (Miller, et al., 1992 J. Urol.147, 956961). Radiographic
progression can be assessed with the use of sequential imaging, and is evidenced by, for example, bone scan identification of two or more new bone lesions with confirmation (according to the Prostate Cancer Clinical Trials Working Group 2 criteria). Response Evaluation Criteria in Solid Tumors (RECIST v 1.1) criteria can also be used to assess radiographic progression of soft tissue lesions. Guidelines for monitoring prostate cancer, including progression of prostate cancer, are described in NCCN Clinical Practice Guidelines in Oncology: Prostate Cancer, version 4.2019, August 19, 2019, the relevant contents of which are incorporated herein by reference in their entirety.
“Castration-resistant prostate cancer” is used interchangeably herein with“androgen- resistant prostate cancer”,“androgen-independent prostate cancer” and“hormone- resistant prostate cancer”.
[00223] “Castration-sensitive prostate cancer” refers to prostate cancer that does not progress (e.g., responds) following administration of one or more ADTs. Progression of prostate cancer can be assessed according to criteria described herein, for example, with respect to“castration-resistant prostate cancer,” and guidelines for monitoring prostate cancer, including progression of prostate cancer, are described in NCCN Clinical Practice Guidelines in Oncology: Prostate Cancer, version 4.2019, August 19, 2019, the relevant contents of which are incorporated herein by reference in their entirety.“Castration-sensitive prostate cancer” is used interchangeably herein with “androgen-sensitive prostate cancer”,“androgen-dependent prostate cancer” and “hormone-sensitive prostate cancer”.
[00224] Further examples of cancers treatable according to the methods described herein include, but are not limited to, Acute Lymphoblastic Leukemia (ALL); Acute Myeloid Leukemia (AML); Adrenocortical Carcinoma; Adrenocortical Carcinoma, Childhood; AIDS-Related Cancer (e.g., Kaposi Sarcoma, AIDS-Related Lymphoma, Primary CNS Lymphoma); Anal Cancer; Appendix Cancer; Astrocytomas, Childhood; Atypical Teratoid/Rhabdoid Tumor, Childhood, Central Nervous System; Basal Cell Carcinoma of the Skin; Bile Duct Cancer; Bladder Cancer; Bladder Cancer, Childhood; Bone Cancer (including Ewing Sarcoma, Osteosarcoma and Malignant Fibrous Histiocytoma); Brain Tumors/Cancer; Breast Cancer; Burkitt Lymphoma; Carcinoid Tumor (Gastrointestinal); Carcinoid Tumor, Childhood; Cardiac (Heart) Tumors, Childhood; Embryonal Tumors, Childhood; Germ Cell Tumor, Childhood; Primary CNS Lymphoma; Cervical Cancer; Childhood Cervical Cancer; Cholangiocarcinoma; Chordoma, Childhood; Chronic Lymphocytic Leukemia (CLL); Chronic Myelogenous Leukemia (CML); Chronic Myeloproliferative Neoplasms; Colorectal Cancer;
Childhood Colorectal Cancer; Craniopharyngioma, Childhood; Cutaneous T-Cell Lymphoma (e.g., Mycosis Fungoides and Sézary Syndrome); Ductal Carcinoma In Situ (DCIS); Embryonal Tumors, Central Nervous System, Childhood; Endometrial Cancer (Uterine Cancer); Ependymoma, Childhood; Esophageal Cancer; Childhood
Esophageal Cancer; Esthesioneuroblastoma; Ewing Sarcoma; Extracranial Germ Cell Tumor, Childhood; Extragonadal Germ Cell Tumor; Eye Cancer; Childhood Intraocular Melanoma; Intraocular Melanoma; Retinoblastoma; Fallopian Tube Cancer; Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma; Gallbladder Cancer; Gastric (Stomach) Cancer; Childhood Gastric (Stomach) Cancer; Gastrointestinal Carcinoid Tumor; Gastrointestinal Stromal Tumors (GIST); Childhood Gastrointestinal Stromal Tumors; Germ Cell Tumors; Childhood Central Nervous System Germ Cell Tumors (e.g., Childhood Extracranial Germ Cell Tumors, Extragonadal Germ Cell Tumors, Ovarian Germ Cell Tumors, Testicular Cancer); Gestational Trophoblastic Disease; Hairy Cell Leukemia; Head and Neck Cancer; Heart Tumors, Childhood;
Hepatocellular (Liver) Cancer; Histiocytosis, Langerhans Cell; Hodgkin Lymphoma; Hypopharyngeal Cancer; Intraocular Melanoma; Childhood Intraocular Melanoma; Islet Cell Tumors, Pancreatic Neuroendocrine Tumors; Kaposi Sarcoma; Kidney (Renal Cell) Cancer; Langerhans Cell Histiocytosis; Laryngeal Cancer; Leukemia; Lip and Oral Cavity Cancer; Liver Cancer; Lung Cancer (Non-Small Cell and Small Cell); Childhood Lung Cancer; Lymphoma; Male Breast Cancer; Malignant Fibrous
Histiocytoma of Bone and Osteosarcoma; Melanoma; Childhood Melanoma;
Melanoma, Intraocular (Eye); Childhood Intraocular Melanoma; Merkel Cell
Carcinoma; Mesothelioma, Malignant; Childhood Mesothelioma; Metastatic Cancer; Metastatic Squamous Neck Cancer with Occult Primary; Midline Tract Carcinoma With NUT Gene Changes; Mouth Cancer; Multiple Endocrine Neoplasia Syndromes; Multiple Myeloma/Plasma Cell Neoplasms; Mycosis Fungoides; Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasms; Myelogenous Leukemia, Chronic (CML); Myeloid Leukemia, Acute (AML); Myeloproliferative Neoplasms, Chronic; Nasal Cavity and Paranasal Sinus Cancer; Nasopharyngeal Cancer;
Neuroblastoma; Non-Hodgkin Lymphoma; Non-Small Cell Lung Cancer; Oral Cancer, Lip and Oral Cavity Cancer and Oropharyngeal Cancer; Osteosarcoma and Malignant Fibrous Histiocytoma of Bone; Ovarian Cancer; Childhood Ovarian Cancer; Pancreatic Cancer; Childhood Pancreatic Cancer; Pancreatic Neuroendocrine Tumors;
Papillomatosis (Childhood Laryngeal); Paraganglioma; Childhood Paraganglioma; Paranasal Sinus and Nasal Cavity Cancer; Parathyroid Cancer; Penile Cancer;
Pharyngeal Cancer; Pheochromocytoma; Childhood Pheochromocytoma; Pituitary Tumor; Plasma Cell Neoplasm/Multiple Myeloma; Pleuropulmonary Blastoma;
Pregnancy and Breast Cancer; Primary Central Nervous System (CNS) Lymphoma; Primary Peritoneal Cancer; Prostate Cancer; Rectal Cancer; Recurrent Cancer; Renal Cell (Kidney) Cancer; Retinoblastoma; Rhabdomyosarcoma, Childhood; Salivary Gland Cancer; Sarcoma (e.g., Childhood Rhabdomyosarcoma, Childhood Vascular Tumors, Ewing Sarcoma, Kaposi Sarcoma, Osteosarcoma (Bone Cancer), Soft Tissue Sarcoma, Uterine Sarcoma); Sézary Syndrome; Skin Cancer; Childhood Skin Cancer; Small Cell Lung Cancer; Small Intestine Cancer; Soft Tissue Sarcoma; Squamous Cell Carcinoma of the Skin; Squamous Neck Cancer with Occult Primary, Metastatic;
Stomach (Gastric) Cancer; Childhood Stomach (Gastric) Cancer; T-Cell Lymphoma, Cutaneous (e.g., Mycosis Fungoides and Sèzary Syndrome); Testicular Cancer;
Childhood Testicular Cancer; Throat Cancer (e.g., Nasopharyngeal Cancer,
Oropharyngeal Cancer, Hypopharyngeal Cancer); Thymoma and Thymic Carcinoma; Thyroid Cancer; Transitional Cell Cancer of the Renal Pelvis and Ureter; Ureter and Renal Pelvis, Transitional Cell Cancer; Urethral Cancer; Uterine Cancer, Endometrial; Uterine Sarcoma; Vaginal Cancer; Childhood Vaginal Cancer; Vascular Tumors;
Vulvar Cancer; and Wilms Tumor and Other Childhood Kidney Tumors.
[00225] Metastases of the aforementioned cancers can also be treated in accordance with the methods described herein. Thus, in some embodiments, the cancer is a metastatic cancer. In other embodiments, the cancer is a primary cancer.
[00226] In some embodiments, the cancer is MCL-1 dependent. As used herein, “MCL-1-dependent” refers to the subset of cancers (e.g., hematologic cancers) wherein myeloid cell leukemia 1 (MCL-1) is the primary driver of suppressing apoptosis.
Typically, MCL-1 dependency promotes blast survival, and is associated with treatment resistance and relapse. MCL-1 dependence can be assessed, for example, by contacting a subject’s cancer cell with a profiling peptide, as described in International Publication Nos. WO 2016/172214 and WO 2018/119000, the relevant contents of which are incorporated herein by reference in their entireties.
[00227] In some embodiments, the cancer is c-Myc-altered. As used herein,“c-Myc- altered” refers to the subset of cancers wherein c-Myc is altered compared to its native sequence, where its expression is amplified compared to an appropriate control (e.g., corresponding normal cells), and where protein levels suggest overexpression of c-Myc. For example, it has been found that c-Myc drives androgen independence in prostate cancer, and overexpression attenuates the anti-tumor activity of androgen receptor suppression. In addition, c-Myc is significantly upregulated in androgen receptor- sensitive prostate cancer. Examples of cancers that can be c-Myc-altered include, but are not limited to, lymphoma (e.g., Burkitt lymphoma, B-cell lymphoma, T-cell lymphoma), cervical cancer, colon cancer, ovarian cancer, breast cancer, lung cancer, prostate cancer, colorectal cancer, pancreatic cancer, gastric cancer and uterine cancer.
[00228] In some embodiments of the methods of treatment, the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, the pharmaceutical composition, or the unit dose form is administered orally.
[00229] Some embodiments provide methods for combination therapies in which an agent known to modulate other pathways, or other components of the same pathway, or even overlapping sets of target enzymes are used in combination with a compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof. In one aspect, such therapy includes the combination of the compound having structure (I), or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof, with a chemotherapeutic agent, therapeutic antibody, and/or radiation treatment, e.g., to provide a synergistic or additive therapeutic effect.
[00230] Many chemotherapeutics are presently known in the art and can be used in combination with a compound having structure (I), or a pharmaceutically acceptable salt or zwitterionic form thereof. In some embodiments, the chemotherapeutic is selected from the group consisting of mitotic inhibitors, alkylating agents, anti- metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, biological response modifiers, anti-hormones, angiogenesis inhibitors, and anti-androgens. [00231] For example, the further therapeutic agent may comprise an alkylating agent, such as chlorambucil, cyclophosphamide, cisplatin; a mitotic inhibitor such as docetaxel (Taxotere; 1,7b,10b-trihydroxy-9-oxo-5b,20-epoxytax-11-ene-2a,4,13a-triyl 4-acetate 2-benzoate 13-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-3- phenylpropanoate}) or paclitaxel; an antimetabolite such as 5-fluorouracil, cytarabine, methotrexate, or pemetrexed; an anti-tumor antibiotic such as daunorubicin or doxorubicin; a corticosteroid such as prednisone or methylprednisone; or a Bcl-2 inhibitor such as venetoclax.
[00232] In certain embodiments, the further therapeutic agent is docetaxel. Docetaxel (trade name TAXOTERE®) is a type of chemotherapeutic agent known as an antimicrotubule agent. Docetaxel is used for treating a variety of cancers, such as metastatic prostate cancer. Docetaxel treatment is often administered intravenously, and often includes premedication with a corticosteroid such as prednisone.
[00233] In certain aspects of all embodiments, the further therapeutic agent is venetoclax (GDC-0199, ABT199, RG7601, trade name VENCLEXTA® or
VENCLYXTO®), which is a Bcl-2 inhibitor that can induce apoptosis in cancer cells. Venetoclax is typically administered orally.
[00234] The further therapeutic agent may be a pharmacological agent that is currently approved by the Food and Drug Administration (FDA) in the U.S. (or elsewhere by any other regulatory body) for use as pharmacological treatment of prostate cancer, or is currently being used experimentally as part of a clinical trial program that relates to prostate cancer. For example, the further therapeutic agents may comprise, without limitation, the chemical entity known as enzalutamide or MDV3100 (4-(3-(4-cyano-3-(trifluoromethyl)phenyl)-5,5-dimethyl-4-oxo-2-thioxoimidazolidin-1- yl)-2-fluoro-N-methylbenzamide) and related compounds; the chemical entity known as TOK 001 and related compounds; the chemical entity known as ARN-509; the chemical entity known as abiraterone (or CB-7630; (3S,8R,9S,10R,13S,14S)-10,13-dimethyl-17- (pyridin-3-yl) 2,3,4,7,8,9,10,11,12,13,14,15-dodecahydro-1H- cyclopenta[a]phenanthren-3-ol), and related molecules; the chemical entity known as bicalutamide (N-[4-cyano-3-(trifluoromethyl)phenyl]-3-[(4-fluorophenyl)sulfonyl]-2- hydroxy-2-methylpropanamide) and related compounds; the chemical entity known as nilutamide (5,5-dimethyl-3-[4-nitro-3-(trifluoromethyl)phenyl] imidazolidine-2,4- dione) and related compounds; the chemical entity known as flutamide (2-methyl-N-[4- nitro-3-(trifluoromethyl)phenyl]-propanamide) and related compounds; the chemical entity known as cyproterone acetate (6-chloro-1b,2b-dihydro-17-hydroxy-3¢H- cyclopropa[1,2]pregna-4,6-diene-3,20-dione) and related compounds, which is currently used to treat prostate cancer, the chemical entity known as docetaxel and related compounds, which is currently used alone or in combination with prednisone to treat prostate cancer, the chemical entity known as bevacizumab (Avastin), a monoclonal antibody that may be used to treat prostate cancer, the chemical entity known as OSU-HDAC42 ((S)-(+)-N-hydroxy-4-(3-methyl-2-phenylbutyrylamino)- benzamide), and related compounds; the chemical entity known as VITAXIN, which may be used to treat prostate cancer, the chemical entity known as sunitumib (N-(2- diethylaminoethyl)-5-[(Z)-(5-fluoro-2-oxo-1H-indol-3-ylidene)methyl]-2,4-dimethyl- 1H-pyrrole-3-carboxamide) and related compounds, which may be used for treatment of prostate cancer, the chemical entity known as ZD-4054 (N-(3-Methoxy-5- methylpyrazin-2-yl)-2-[4-(1,3,4-oxadiazol-2-yl)phenyl]pyridin-3-sulfonamid) and related compounds; the chemical entity known as VN/124-1 (3b-Hydroxy-17-(1H- benzimidazol-1-yl)androsta-5,16-diene), and related compounds; the chemical entity known as cabazitaxel (XRP-6258), and related compounds; the chemical entity known as MDX-010 (Ipilimumab); the chemical entity known as OGX 427; the chemical entity known as OGX 011; the chemical entity known as finasteride (Proscar, Propecia; N- (1,1-dimethylethyl)-3-oxo-(5a,17b)-4-azaandrost-1-ene-17-carboxamide), and related compounds; the chemical entity known as dutasteride (Avodart; 5a, 17b)-N-{2,5 bis(trifluoromethyl) phenyl}-3-oxo-4-azaandrost-1-ene-17-carboxamide) and related compounds; the chemical entity known as turosteride ((4aR,4bS,6aS,7S,9aS,9bS,11aR)- 1,4a,6a-trimethyl-2-oxo-N-(propan-2-yl)-N-(propan-2 ylcarbamoyl)hexadecahydro-1H- indeno[5,4-f]quinoline-7-carboxamide), and related compounds; the chemical entity known as bexlosteride (LY-191,704; (4aS,10bR)-8-chloro-4-methyl-1,2,4a,5,6,10b- hexahydrobenzo[f]quinolin-3-one), and related compounds; the chemical entity known as izonsteride (LY-320,236; (4aR,10bR)-8-[(4-ethyl-1,3-benzothiazol-2-yl)sulfanyl]- 4,10b-dimethyl-1,4,4a,5,6,10b-hexahydrobenzo[f]quinolin-3(2H)-one) and related compounds; the chemical entity known as FCE 28260 and related compounds; the chemical entity known as SKF105,111, and related compounds; the chemical entity known as AZD3514; the chemical entity known as EZN-4176; the chemical entity known as ODM-201, sipuleucel-T, cabazitaxel; a combination of bevacizumab, docetaxel, thalidomide and prednisone; and/or abiraterone. In certain aspects of all embodiments, the further therapeutic agent is an androgen receptor antagonist that blocks androgen binding to androgen receptor. Examples of therapies that block androgen binding to androgen receptor include enzalutamide and apalutamide. In particular embodiments, the further therapeutic agent is enzalutamide. Enzalutamide (trade name XTANDI®) is an androgen receptor (AR) antagonist that is used for treating non-metastatic castration-resistant prostate cancer and metastatic castration- resistant prostate cancer. Enzalutamide treatment may be combined with castration (surgical or chemical).
[00235] In certain aspects of all embodiments, the further therapeutic agent is abiraterone. Abiraterone (trade name ZYTIGA®) is a CYP17A1 inhibitor, which significantly decreases testosterone production. Abiraterone treatment may be combined with other further therapies, such as a corticosteroid (e.g., prednisone) and/or castration (surgical or chemical).
[00236] In certain aspects of all embodiments, the further therapeutic agent is selected from at least one of: a bromodomain inhibitor, a histone methyltransferase inhibitor, a histone deacetylase inhibitor, or a histone demethylases inhibitor.
[00237] In certain aspects of all embodiments, the further therapeutic agent is a bromodomain inhibitor, for example, an inhibitor of a bromodomain protein such as Brd2, Brd3, Brd4 and/or BrdT. In particular embodiments, the further therapeutic agent comprises a BRD4 inhibitor. In some of these embodiments, the further therapeutic agent is JQ-1 (Nature 2010 Dec 23;468(7327):1067-73), BI2536 (ACS Chem. Biol. 2014 May 16;9(5):1160-71; Boehringer Ingelheim), TG101209 (ACS Chem. Biol.2014 May 16;9(5):1160-71), OTX015 (Mol. Cancer Ther. November 201312; C244;
Oncoethix), IBET762 (J Med Chem.2013 Oct 10;56(19):7498-500; GlaxoSmithKline), IBET151 (Bioorg. Med. Chem. Lett.2012 Apr 15;22(8):2968-72; GlaxoSmithKline), PFI-1 (J. Med. Chem.2012 Nov 26;55(22):9831-7; Cancer Res.2013 Jun
1;73(11):3336-46; Structural Genomics Consortium) or CPI-0610 (Constellation Pharmaceuticals). In other embodiments, the BRD inhibitor is IBET 762 (GSK525762), TEN-010 (Tensha Therapeutics), CPI-203 (Leukemia.28 (10): 2049–59, 2014), RVX- 208 (Proceedings of the National Academy of Sciences of the United States of America. 110 (49): 19754–9, 2013), LY294002 (ACS Chemical Biology.9 (2): 495–502, 2014), AZD5153 (Journal of Medicinal Chemistry.59 (17): 7801–17, 2016), MT-1 (Nature Chemical Biology.12 (12): 1089–10962016) or MS645 (Proceedings of the National Academy of Sciences of the United States of America.115 (31): 7949–7954, 2018).
[00238] In certain aspects of all embodiments, the further therapeutic agent is a histone methyltransferase inhibitor. In some of these embodiments, the further therapeutic agent comprises a DOT1-like histone methyltransferase (DOT1L) inhibitor. DOT1L is a histone methyltransferase enzyme that targets lysine 79 in the globular domain of histone H3 for mono-, di-, or trimethylation. In some of these embodiments, the further therapeutic agent is EPZ004777, EPZ-5676 (Blood.2013 Aug
8;122(6):1017-25) or SGC0946 (Nat. Commun.2012;3:1288), for example, EPZ-5676.
[00239] In certain aspects of all embodiments, the further therapeutic agent is a histone deacetylase (HDAC) inhibitor. HDAC proteins may be grouped into classes based on homology to yeast HDAC proteins with Class I made up of HDAC1, HDAC2, HDAC3 and HDAC 8; Class IIa made up of HDAC4, HDAC5, HDAC7 and HDAC 9; Class IIb made up of HDAC6 and HDAC10; and Class IV made up of HDAC11. In some of these embodiments, the further therapeutic agent is trichostatin A, vorinostat (Proc. Natl. Acad. Sci. U.S.A.1998 Mar 17;95(6):3003-7), givinostat, abexinostat (Mol. Cancer Ther.2006 May;5(5):1309-17), belinostat (Mol. Cancer Ther.2003
Aug;2(8):721-8), panobinostat (Clin. Cancer Res.2006 Aug 1;12(15):4628-35), resminostat (Clin. Cancer Res.2013 Oct 1;19(19):5494-504), quisinostat (Clin. Cancer Res.2013 Aug 1;19(15):4262-72), depsipeptide (Blood.2001 Nov 1;98(9):2865-8), entinostat (Proc. Natl. Acad. Sci. U.S.A.1999 Apr 13;96(8):4592-7), mocetinostat (Bioorg. Med. Chem. Lett.2008 Feb 1;18(3):1067-71) or valproic acid (EMBO J.2001 Dec 17;20(24):6969-78). For example, in some embodiments, the further therapeutic agent is panobinostat. In other embodiments, the further therapeutic agent is panobinostat or SAHA.
[00240] In certain aspects of all embodiments, the further therapeutic agent is a histone demethylase inhibitor. In particular embodiments, the histone demethylase inhibitor is a lysine-specific demethylase 1A (Lsd1) inhibitor. In some of these embodiments, the further therapeutic agent is HCI-2509 (BMC Cancer.2014 Oct 9;14:752), tranylcypromine or ORY-1001 (J. Clin. Oncol 31, 2013 (suppl; abstr e13543). In other embodiments, the further therapeutic agent is HCI-2509.
[00241] In certain aspects of all embodiments, the further therapeutic agent is a MLL-menin inhibitor. Menin is a co-factor of the oncogenic MLL fusion protein, and an MLL-menin inhibitor blocks the interaction of the two proteins. Examples of MLL- menin inhibitors include MI-453, M-525, and MI-503.
[00242] In certain aspects of all embodiments, the further therapeutic agent is a B- cell receptor signaling antagonist (e.g., a Bruton’s tyrosine kinase (BTK) inhibitor, such as ibrutinib).
[00243] In certain aspects of all embodiments, the further therapeutic agents is an immunomodulator. Immunomodulators of particular interest for use in combination with compounds of the present disclosure include: afutuzumab (available from
ROCHE®); pegfilgrastim (NEULASTA®); lenalidomide (CC-5013, REVLIMID®); thalidomide (THALOMID®); actimid (CC4047); and IRX-2 (mixture of human cytokines including interleukin 1, interleukin 2, and interferon g, CAS 951209-71-5, available from IRX Therapeutics).
[00244] In certain aspects of all embodiments, the further therapeutic agent comprises a chimeric antigen receptor T-cell (CAR-T) therapy. CAR-T therapies of particular interest for use in combination with compounds of the present disclosure include: tisagenlecleucel (Novartis), axicabtagene ciloleucel (Kite), and tocilizumab and atlizumab (Roche).
[00245] In certain aspects of all embodiments, the further therapeutic agent is an immune checkpoint inhibitor (e.g., a PD-1 inhibitor, such as pembrolizumab or nivolumab; a PD-L1 inhibitor, such as atezolizumab, avelumab, or durvalumab; a CTLA-4 inhibitor; a LAG-3 inhibitor; or a Tim-3 inhibitor). Other immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure include: PD-1 inhibitors, such as pembrolizumab (KEYTRUDA®), nivolumab
(OPDIVO®), cemiplimab (LIBTAYO®), spartalizumab (PDR001), pidilizumab (CureTech), MEDI0680 (Medimmune), cemiplimab (REGN2810), dostarlimab (TSR- 042), PF-06801591 (Pfizer), tislelizumab (BGB-A317), camrelizumab (INCSHR1210, SHR-1210), and AMP-224 (Amplimmune); PD-L1 inhibitors, such as atezolizumab (TECENTRIQ®), avelumab (BAVENCIO®), durvalumab (IMFINZI®), FAZ053 (Novartis), and BMS-936559 (Bristol-Myers Squibb); and drugs that target CTLA-4, such as ipilimumab (YERVOY®).
[00246] In various embodiments, the immune checkpoint inhibitor is a PD-1 inhibitor. In specific embodiments, the PD-1 inhibitor is pembrolizumab, nivolumab, or a combination thereof. In particular embodiments, the PD-1 inhibitor is pembrolizumab (also known as lambrolizumab, MK-3475, MK03475, SCH-900475, or
KEYTRUDA®). Pembrolizumab and other anti-PD-1 antibodies are disclosed in Hamid, O., et al. (2013) New England Journal of Medicine 369 (2): 134–44, US 8,354,509, and WO 2009/114335, incorporated by reference in their entireties. In particular embodiments, the PD-1 inhibitor is nivolumab (also known as MDX-1106, MDX-1106-04, ONO-4538, BMS-936558, or OPDIVO®). Nivolumab (clone 5C4) and other anti-PD-1 antibodies are disclosed in US 8,008,449 and WO 2006/121168, incorporated by reference in their entireties. In some other embodiments, the PD-1 inhibitor is AMP-224 (Amplimmune), CBT-501 (CBT Pharmaceuticals), CBT-502 (CBT Pharmaceuticals), JS001 (Junshi Biosciences), IBI308 (Innovent Biologics), INCSHR1210 (Incyte), also known as SHR-1210 (Hengrui Medicine), BGBA317 (Beigene), BGB-108 (Beigene), BAT-I306 (Bio-Thera Solutions), GLS-010 (Gloria Pharmaceuticals; WuXi Biologics), AK103, AK104, AK105 (Akesio Biopharma;
Hangzhou Hansi Biologics; Hanzhong Biologics), LZM009 (Livzon), HLX-10 (Henlius Biotech), MEDI0680 (Medimmune), PDF001 (Novartis), PF-06801591 (Pfizer), pidilizumab (CureTech), REGN2810 (Regeneron), TSR-042 (Tesaro), also known as ANB011, or CS1003 (CStone Pharmaceuticals). MEDI0680 (Medimmune) is also known as AMP-514. MEDI0680 and other anti- PD-1 antibodies are disclosed in US 9,205,148 and WO 2012/145493, incorporated by reference in their entireties.
Pidilizumab is also known as CT-011. Pidilizumab and other anti-PD-1 antibodies are disclosed in Rosenblatt, J., et al. (2011) J Immunotherapy 34(5): 409-18, US 7,695,715, US 7,332,582, and US 8,686,119, incorporated by reference in their entireties.
[00247] In one embodiment, the anti-PD-1 antibody molecule is cemiplimab. In one embodiment, the anti-PD-1 antibody molecule is sintilimab. In one embodiment, the anti-PD-1 antibody molecule is toripalimab. In one embodiment, the anti-PD-1 antibody molecule is camrelizumab. [00248] Further known anti-PD-1 antibody molecules include those described, e.g., in WO 2015/112800, WO 2016/092419, WO 2015/085847, WO 2014/179664, WO 2014/194302, WO 2014/209804, WO 2015/200119, US 8,735,553, US 7,488,802, US 8,927,697, US 8,993,731, and US 9,102,727, incorporated by reference in their entireties.
[00249] In one embodiment, the PD-1 inhibitor is an anti-PD-1 antibody molecule as described in US 2015/0210769. In one embodiment, the anti-PD-1 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP049- Clone-E or BAP049-Clone-B disclosed in US 2015/0210769. The antibody molecules described herein can be made by vectors, host cells, and methods described in US 2015/0210769, incorporated by reference in its entirety.
[00250] In one embodiment, the PD-1 inhibitor is a peptide that inhibits the PD-1 signaling pathway, e.g., as described in US 8,907,053, incorporated by reference in its entirety. In one embodiment, the PD-1 inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PD-L1 or PD- L2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence). In one embodiment, the PD-1 inhibitor is AMP-224 (B7-DCIg (Amplimmune), e.g., disclosed in WO 2010/027827 and WO 2011/066342, incorporated by reference in their entireties).
[00251] In some embodiments, the immune checkpoint inhibitor is a PD-L1 inhibitor. In some such embodiments, the PD-L1 inhibitor is atezolizumab, avelumab, durvalumab, or a combination thereof. In particular embodiments, the PD-L1 inhibitor is atezolizumab, also known as MPDL3280A, RG7446, RO5541267, YW243.55.S70, or TECENTRIQ™. Atezolizumab and other anti-PD-L1 antibodies are disclosed in US 8,217,149, incorporated by reference in its entirety. In particular embodiments, the PD- L1 inhibitor is avelumab, also known as MSB0010718C. Avelumab and other anti-PD- L1 antibodies are disclosed in WO 2013/079174, incorporated by reference in its entirety. In particular embodiments, the PD-L1 inhibitor is durvalumab, also known as MEDI4736. Durvalumab and other anti-PD-L1 antibodies are disclosed in US
8,779,108, incorporated by reference in its entirety. In certain embodiments, the PD-L1 inhibitor is KN035 (Alphamab; 3DMed), BMS 936559 (Bristol-Myers Squibb), CS1001 (CStone Pharmaceuticals), FAZ053 (Novartis), SHR-1316 (Hengrui Medicine), TQB2450 (Chiatai Tianqing), STI-A1014 (Zhaoke Pharm; Lee's Pharm), BGB-A333 (Beigene), MSB2311 (Mabspace Biosciences), or HLX-20 (Henlius Biotech). In one embodiment, the anti-PD-L1 antibody molecule is BMS-936559 (Bristol-Myers Squibb), also known as MDX-1105 or 12A4. BMS-936559 and other anti-PD-L1 antibodies are disclosed in US 7,943,743 and WO 2015/081158, incorporated by reference in their entireties. In some embodiments, the PD-L1 inhibitor is a monoclonal antibody (e.g., as made by Hisun Pharm and applying for clinical trials).
[00252] In one embodiment, the PD-L1 inhibitor is an anti-PD-L1 antibody molecule. In one embodiment, the PD-L1 inhibitor is an anti-PD-L1 antibody molecule as disclosed in US 2016/0108123, incorporated by reference in its entirety. In one embodiment, the anti-PD-L1 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP058-Clone O or BAP058-Clone N disclosed in US 2016/0108123.
[00253] Further known anti-PD-L1 antibodies include those described, e.g., in WO 2015/181342, WO 2014/100079, WO 2016/000619, WO 2014/022758, WO
2014/055897, WO 2015/061668, WO 2013/079174, WO 2012/145493, WO
2015/112805, WO 2015/109124, WO 2015/195163, US 8,168,179, US 8,552,154, US 8,460,927, and US 9,175,082, incorporated by reference in their entireties.
[00254] In some embodiments, the immune checkpoint inhibitor is a CTLA-4 inhibitor. In certain embodiments, the CTLA-4 inhibitor is ipilimumab. In other embodiments, the CTLA4 inhibitor is tremelimumab.
[00255] In some embodiments, the immune checkpoint inhibitor is a LAG-3 inhibitor. In some embodiments, the LAG-3 inhibitor is chosen from LAG525
(Novartis), BMS-986016 (Bristol-Myers Squibb), or TSR-033 (Tesaro). In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule. In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule as disclosed in US 2015/0259420, incorporated by reference in its entirety. In one embodiment, the anti-LAG-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP050-Clone I or BAP050-Clone J disclosed in US
2015/0259420. [00256] In one embodiment, the anti-LAG-3 antibody molecule is BMS-986016 (Bristol-Myers Squibb), also known as BMS986016. BMS-986016 and other anti-LAG- 3 antibodies are disclosed in WO 2015/116539 and US 9,505,839, incorporated by reference in their entireties. In one embodiment, the anti-LAG-3 antibody molecule is TSR-033 (Tesaro). In one embodiment, the anti-LAG-3 antibody molecule is IMP731 or GSK2831781 (GSK and Prima BioMed). IMP731 and other anti-LAG-3 antibodies are disclosed in WO 2008/132601 and US 9,244,059, incorporated by reference in their entireties. In one embodiment, the anti-LAG-3 antibody molecule is IMP761 (Prima BioMed).
[00257] Further known anti-LAG-3 antibodies include those described, e.g., in WO 2008/132601, WO 2010/019570, WO 2014/140180, WO 2015/116539, WO
2015/200119, WO 2016/028672, US 9,244,059, US 9,505,839, incorporated by reference in their entireties.
[00258] In one embodiment, the anti-LAG-3 inhibitor is a soluble LAG-3 protein, e.g., IMP321 (Prima BioMed), e.g., as disclosed in WO 2009/044273, incorporated by reference in its entirety.
[00259] In some embodiments, the immune checkpoint inhibitor is a TIM-3 inhibitor. In some embodiments, the TIM-3 inhibitor is MGB453 (Novartis) or TSR- 022 (Tesaro).
[00260] In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule. In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule as disclosed in US 2015/0218274, incorporated by reference in its entirety. In one embodiment, the anti-TIM-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of ABTIM3-hum11 or ABTIM3-hum03 disclosed in US 2015/0218274.
[00261] In one embodiment, the anti-TIM-3 antibody molecule is TSR-022
(AnaptysBio/Tesaro). In one embodiment, the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or light chain sequence of APE5137 or APE5121. APE5137, APE5121, and other anti- TIM-3 antibodies are disclosed in WO 2016/161270, incorporated by reference in its entirety. In one embodiment, the anti-TIM-3 antibody molecule is the antibody clone F38-2E2. [00262] Further known anti-TIM-3 antibodies include those described, e.g., in WO 2016/111947, WO 2016/071448, WO 2016/144803, US 8,552,156, US 8,841,418, and US 9,163,087, incorporated by reference in their entireties.
[00263] In an effort to protect normal cells from treatment toxicity and to limit organ toxicities, cytoprotective agents (such as neuroprotectants, free-radical scavengers, cardioprotectors, anthracycline extravasation neutralizers, nutrients and the like) may be used as an adjunct therapy in combination with compounds of the present disclosure. Suitable cytoprotective agents include amifostine (ETHYOL®), glutamine, dimesna (TAVOCEPT®), mesna (MESNEX®), dexrazoxane (ZINECARD® or TOTECT®), xaliproden (XAPRILA®), and leucovorin (also known as calcium leucovorin, citrovorum factor and folinic acid).
[00264] Some patients may experience allergic reactions to compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) during or after administration. Therefore, anti-allergic agents can be administered in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti- cancer agent(s)) to minimize the risk of an allergic reaction. Suitable anti-allergic agents include corticosteroids (Knutson, S., et al., PLoS One,
DOI:10.1371/journal.pone.0111840 (2014)), such as dexamethasone (e.g.,
DECADRON®), beclomethasone (e.g., BECLOVENT®), hydrocortisone (also known as cortisone, hydrocortisone sodium succinate, hydrocortisone sodium phosphate, sold under the tradenames ALA-CORT®, hydrocortisone phosphate, SOLU-CORTEF®, HYDROCORT ACETATE® and LANACORT®), prednisolone (sold under the tradenames DELTA-CORTEL®, ORAPRED®, PEDIAPRED® and PRELONE®), prednisone (sold under the tradenames DELTASONE®, LIQUID RED®,
METICORTEN® and ORASONE®), methylprednisolone (also known as 6- methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, sold under the tradenames DURALONE®, MEDRALONE®, MEDROL®, M- PREDNISOL® and SOLU-MEDROL®); antihistamines, such as diphenhydramine (e.g., BENADRYL®), hydroxyzine, and cyproheptadine; and bronchodilators, such as the beta-adrenergic receptor agonists, albuterol (e.g., PROVENTIL®), and terbutaline (BRETHINE®). [00265] Some patients may experience nausea during and after administration of the compounds described herein and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)). Therefore, anti-emetics can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) to prevent nausea (upper stomach) and vomiting. Suitable anti-emetics include aprepitant (EMEND®), ondansetron (ZOFRAN®), granisetron HCl (KYTRIL®), lorazepam (ATIVAN®, dexamethasone (DECADRON®), prochlorperazine (COMPAZINE®), casopitant (REZONIC® and ZUNRISA®), and combinations thereof.
[00266] Medication to alleviate the pain experienced during treatment is often prescribed to make the patient more comfortable. Common over-the-counter analgesics, such TYLENOL®, can also be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)). Opioid analgesic drugs such as hydrocodone/paracetamol or hydrocodone/acetaminophen (e.g., VICODIN®), morphine (e.g., ASTRAMORPH® or AVINZA®), oxycodone (e.g., OXYCONTIN® or PERCOCET®), oxymorphone hydrochloride (OPANA®), and fentanyl (e.g., DURAGESIC®) can be useful for moderate or severe pain, and can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)). EMBODIMENTS
[00267] Embodiment 1. A polymorph of a compound having the following structure (I):
Figure imgf000070_0001
,
(I)
or a tautomer or zwitterionic form thereof, the polymorph having an X- ray powder diffraction pattern comprising the following:
D space (Å):
18.3 ± 0.09 8.1 ± 0.06
6.4 ± 0.08
5.9 ± 0.06
4.4 ± 0.05
expressed in terms of "D" spacing.
[00268] Embodiment 2. The polymorph of Embodiment 1, wherein the X-ray powder diffraction pattern comprises the following: D space (Å):
18.38 ± 0.003
8.15 ± 0.008
6.47 ± 0.002
5.95 ± 0.007
4.44 ± 0.006
expressed in terms of "D" spacing.
[00269] Embodiment 3. The polymorph of Embodiment 1, wherein the X-ray powder diffraction pattern comprises the following: D space (Å):
18.382
8.157
6.472
5.956
4.445
expressed in terms of "D" spacing.
[00270] Embodiment 4. A polymorph of a compound having the following structure (I):
Figure imgf000071_0001
, (I)
or a tautomer or zwitterion thereof, the polymorph being a crystalized form having a monoclinic space group P21 with lattice parameters of:
Figure imgf000072_0003
[00271] Embodiment 5. A polymorph of a compound having the following structure (I):
Figure imgf000072_0001
or a tautomer or zwitterionic form thereof, wherein the polymorph has the X-ray diffraction pattern set forth in Figure 1.
[00272] Embodiment 6. A polymorph of a compound having the following structure (I):
Figure imgf000072_0002
or a tautomer or zwitterionic form thereof, wherein the polymorph is Form B. [00273] Embodiment 7. A polymorph of a compound having the following
Figure imgf000073_0002
or a tautomer or zwitterionic form thereof wherein the polymorph is formed by a method comprising:
a) contacting an amorphous compound of structure (I) with a lattice forming reagent; and
b) treating the product of step a) with a solvent having water content less than about 0.05 % v/v and removing the solvent, thereby forming the polymorph.
[00274] Embodiment 8. The polymorph of Embodiment 7, wherein the lattice forming reagent is maleic acid.
[00275] Embodiment 9. The polymorph of Embodiment 8, wherein the maleic acid is added at a ratio of 1:1 ± 0.2 of amorphous compound to maleic acid.
[00276] Embodiment 10. The polymorph of any one of Embodiments 7-9, wherein the solvent is ethanol or tetrahydrofuran.
[00277] Embodiment 11. The polymorph of any one of Embodiments 7-10, wherein the contacting further comprises suspending the amorphous compound of structure (I) in aqueous tetrahydrofuran.
[00278] Embodiment 12. A polymorph of a compound having the following structure (I):
Figure imgf000073_0001
or a tautomer or zwitterionic form thereof, wherein the polymorph has an initial purity of at least 99.5% and a subsequent purity of at least 99.5% after being stored from about 12 hours up to about 7 days at about 25°C ± 2°C at a relative humidity of 60%.
[00279] Embodiment 13. The polymorph of Embodiment 12, wherein the subsequent purity is at least 99.5% after being stored for greater than about 7 days at about 25°C ± 2°C at a relative humidity of 60%.
[00280] Embodiment 14. The polymorph of Embodiment 12 or 13, wherein the subsequent purity is at least 99.5% after being stored for greater than about 30 days at about 25°C ± 2°C at a relative humidity of 60%.
[00281] Embodiment 15. The polymorph of any one of Embodiments 12-14, wherein the initial purity and subsequent purity are as determined by HPLC.
[00282] Embodiment 16. A polymorph of a compound having the following structure (I):
Figure imgf000074_0001
( )
or a tautomer or zwitterionic form thereof, wherein the polymorph has an endotherm peak value at about 256°C– 268°C as determined by differential scanning calorimetry.
[00283] Embodiment 17. The polymorph of Embodiment 16, wherein the endotherm peak value is at about 257.0°C– 266.0°C.
[00284] Embodiment 18. The polymorph of Embodiment 16 or 17, wherein the endotherm peak value is at about 258.0°C– 265.0.
[00285] Embodiment 19. The polymorph of any one of claims 1-18, wherein the polymorph comprises a zwitterionic form having the following structure (II): .
Figure imgf000075_0001
[00286] Embodiment 20. A pharmaceutical composition comprising the polymorph of any one of Embodiments 1-19 and a pharmaceutically acceptable carrier or excipient.
[00287] Embodiment 21. The pharmaceutical composition of Embodiment 20, wherein the pharmaceutical composition is formulated for oral administration.
[00288] Embodiment 22. The pharmaceutical composition of Embodiment 20 or 21, wherein the pharmaceutical composition comprises the polymorph in a
concentration ranging from about 0.5 wt.% to about 11.25 wt.%.
[00289] Embodiment 23. The pharmaceutical composition of any one of
Embodiments 20-22, wherein the pharmaceutical composition comprises the polymorph in a concentration ranging from about 0.6 wt.% to about 11.05 wt.%.
[00290] Embodiment 24. The pharmaceutical composition of any one of
Embodiments 20-23, wherein the pharmaceutical composition comprises about 0.6 wt.% of the polymorph.
[00291] Embodiment 25. The pharmaceutical composition of any one of
Embodiments 20-23, wherein the pharmaceutical composition comprises about 2.5 wt.% of the polymorph.
[00292] Embodiment 26. The pharmaceutical composition of any one of
Embodiments 20-23, wherein the pharmaceutical composition comprises about 11.0 wt.% of the polymorph.
[00293] Embodiment 27. The pharmaceutical composition of any one of
Embodiments 20-26, wherein the pharmaceutical composition comprises about 1 milligram (mg) of the polymorph.
[00294] Embodiment 28. The pharmaceutical composition of any one of
Embodiments 20-26, wherein the pharmaceutical composition comprises about 4 mg of the polymorph. [00295] Embodiment 29. The pharmaceutical composition of any one of
Embodiments 20-26, wherein the pharmaceutical composition comprises about 16 mg of the polymorph.
[00296] Embodiment 30. The pharmaceutical composition of any one of
Embodiments 20-29, wherein the excipient is anhydrous lactose or microcrystalline cellulose.
[00297] Embodiment 31. The pharmaceutical composition of any one of
Embodiments 20-30, wherein the excipient is anhydrous lactose.
[00298] Embodiment 32. The pharmaceutical composition of any one of
Embodiments 20-30, wherein the excipient is microcrystalline cellulose.
[00299] Embodiment 33. The pharmaceutical composition of any one of
Embodiments 20-32, wherein the pharmaceutical composition comprises the excipient in a concentration ranging from about 85 wt.% to about 98 wt.%.
[00300] Embodiment 34. The pharmaceutical composition of any one of
Embodiments 20-33, wherein the pharmaceutical composition comprises the excipient in a concentration ranging from about 87 wt.% to about 97.5 wt.%.
[00301] Embodiment 35. The pharmaceutical composition of any one of
Embodiments 20-34, wherein the pharmaceutical composition comprises about 87 wt.% of the excipient.
[00302] Embodiment 36. The pharmaceutical composition of any one of
Embodiments 20-34, wherein the pharmaceutical composition comprises about 95.5 wt.% of the excipient.
[00303] Embodiment 37. The pharmaceutical composition of any one of
Embodiments 20-34, wherein the pharmaceutical composition comprises about 97.5 wt.% of the excipient.
[00304] Embodiment 38. The pharmaceutical composition of any one of
Embodiments 20-37, further comprising colloidal silicon dioxide.
[00305] Embodiment 39. The pharmaceutical composition of Embodiment 38, wherein the pharmaceutical composition comprises about 1 wt.% of the colloidal silicon dioxide.
[00306] Embodiment 40. The pharmaceutical composition of any one of
Embodiments 20-39 further comprising magnesium stearate. [00307] Embodiment 41. The pharmaceutical composition of Embodiment 40, wherein the pharmaceutical composition comprises about 1 wt.% of the magnesium stearate.
[00308] Embodiment 42. The pharmaceutical composition of any one of
Embodiments 20-41, in the form of a capsule for oral administration.
[00309] Embodiment 43. A pharmaceutical composition comprising a polymorph of any one of Embodiments 1-19 having water content less than 0.50 % as determined by Karl Fischer titration.
[00310] Embodiment 44. A unit dose form comprising a pharmaceutical composition of any one of Embodiments 20-43.
[00311] Embodiment 45. A method for preparing a polymorph, the method comprising: a) contacting an amorphous compound having the following structure (I):
Figure imgf000077_0001
,
(I)
with a lattice forming reagent; and
b) treating the product of step a) with solvent having water content less than about 0.05 % v/v; and removing the solvent, thereby forming the polymorph.
[00312] Embodiment 46. The method of Embodiment 45, wherein the lattice forming reagent is an acid.
[00313] Embodiment 47. The method of Embodiment 46, wherein the acid is selected from the group consisting of maleic acid, fumaric acid, L-tartaric acid, hippuric acid, nicotinic acid, acetic acid, and combinations thereof.
[00314] Embodiment 48. The method of any one of Embodiments 45-47, wherein the lattice forming reagent is maleic acid. [00315] Embodiment 49. The method of Embodiment 45, wherein the lattice forming reagent is aspartame.
[00316] Embodiment 50. The method of Embodiment 45, wherein the lattice forming reagent is D-xylose.
[00317] Embodiment 51. The method of any one of Embodiments 45-50, wherein the removing the solvent is at a pressure less than about 1 atm and a temperature greater than about 35°C.
[00318] Embodiment 52. The method of any one of Embodiments 45-51, wherein the method further comprises preparing a compound of structure (III):
Figure imgf000078_0002
(III)
by reacting a compound having the following structure:
Figure imgf000078_0003
or a salt thereof, with a base and a compound having the following structure:
Figure imgf000078_0001
.
[00319] Embodiment 53. The method of Embodiment 52, wherein the base is an amine base.
[00320] Embodiment 54. The method of Embodiment 52 or 53, wherein the base is triethylamine or diisopropylethyl amine.
[00321] Embodiment 55. The method of any one of Embodiments 52-54, wherein the method further comprises preparing the amorphous compound of structure (I):
Figure imgf000079_0001
,
(I)
by reacting the compound of structure (III), or a salt thereof, with a phosphoester-cleaving compound and treating with a basic solution.
[00322] Embodiment 56. The method of Embodiment 55, wherein the
phosphoester-cleaving compound is trimethyl silyl bromide (TMSBr), and the basic solution comprises ammonium bicarbonate.
[00323] Embodiment 57. The method of any one of Embodiments 45-56, wherein the polymorph is a polymorph according to any one of Embodiments 1-19.
[00324] Embodiment 58. A polymorph prepared according to the method of any one of Embodiments 45-57.
[00325] Embodiment 59. A method for treating a disease associated with overexpression of a cyclin-dependent kinase (CDK) in a mammal in need thereof, the method comprising administering a therapeutically effective amount of the polymorph of any one of Embodiments 1-19 or 58, the pharmaceutical composition of any one of Embodiments 20-43, or the unit dose form of Embodiment 43 to the mammal.
[00326] Embodiment 60. The method of Embodiment 59, wherein the disease is cancer.
[00327] Embodiment 61. The method of Embodiment 60, wherein the cancer is a hematologic cancer.
[00328] Embodiment 62. The method of Embodiment 60, wherein the hematologic cancer is selected from acute myelogenous leukemia (AML), follicular lymphoma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), multiple myeloma (MM), and non-Hodgkin’s lymphoma.
[00329] Embodiment 63. The method of Embodiment 62, wherein the
hematological cancer is acute myelogenous leukemia (AML).
[00330] Embodiment 64. The method of Embodiment 62, wherein the hematologic cancer is chronic lymphocytic leukemia (CLL). [00331] Embodiment 65. The method of Embodiment 62, wherein the hematologic cancer is myelodysplasic syndrome (MDS).
[00332] Embodiment 66. The method of Embodiment 62, wherein the hematologic cancer is multiple myeloma (MM).
[00333] Embodiment 67. The method of Embodiment 60, wherein the cancer comprises a solid tumor.
[00334] Embodiment 68. The method of Embodiment 60 or 67, wherein the cancer is bladder cancer.
[00335] Embodiment 69. The method of Embodiment 60 or 67, wherein the cancer is lung cancer.
[00336] Embodiment 70. The method of Embodiment 60 or 67, wherein the cancer is liver cancer.
[00337] Embodiment 71. The method of Embodiment 60 or 67, wherein the cancer is prostate cancer.
[00338] Embodiment 72. The method of any one of Embodiments 60-71, wherein the polymorph, the pharmaceutical composition, or the unit dose form is administered orally.
[00339] The examples and preparations provided below further illustrate and exemplify polymorph of a compound of structure (I), and methods of preparing the same. It is to be understood that the scope of the present invention is not limited in any way by the scope of the following examples and preparations. In the following examples, and throughout the specification and claims, molecules with a single stereocenter, unless otherwise noted, exist as a racemic mixture. Those molecules with two or more stereocenters, unless otherwise noted, exist as a racemic mixture of diastereomers. Single enantiomers/diastereomers may be obtained by methods known to those skilled in the art.
EXAMPLES
[00340] Data was acquired according to the parameters listed below: X-ray powder diffraction (XRPD): [00341] Stoe Stadi P. Copper KaI radiation, 40kV / 40mA; Mythen 1K detector transmission mode, curved monochromator, 0.02°2q step size, 12 s step time, 1.5- 50.5°2q scanning range with 1°2q detector step in step-scan mode. Each sample (25-40 mg of powder) was placed between two cellulose acetate foils spaced with a metal washer (0.4 mm thick, 12-mm inner diameter; "sandwich element"). The sandwich element was transferred to a sample holder (SCell) that was sealed with acetate foils. Samples were acquired in ambient air atmosphere and rotated during measurements. TG-FTIR:
[00342] Netzsch Thermo-Microbalance TG 209 with Bruker FT-IR Spectrometer IFS28 or Vector 22; Al crucible with microhole, N2 atmosphere, 10 K/min heating rate, 25°C to 300°C (or 350°C range). HPLC:
[00343] The method used to detect and determine purity of compound of structure (I) and related substances (such as alvocidib) was a reverse-phase HPLC method with a gradient program and DAD detection technique. Reverse phase C18 Waters X-bridge 150 mm × 4.6 mm, 3.5-µm particle column; flow rate = 1.0 mL/min; detection wavelength = 265 nm; run time: 35.0 minutes; sample diluted in methanol; mobile phase A was 80:20 (v/v) pH 6.5 buffered aqueous acetonitrile; mobile phase B was 35:65 (v/v) pH 6.5 buffered aqueous acetonitrile; 1.0 mL/min; column temperature = 35°C. The gradient program is depicted in the following table:
Figure imgf000081_0001
[00344] Total Impurities (%) was calculated by summing the percentages of each individual impurity, including alvocidib. Other Impurities (%) was calculated by summing the percentages of each individual impurity, excluding alvocidib. Purity of compound of structure (I) (%) was calculated by taking the difference between 100% and the Total Impurities (%). All individual impurities at and above 0.05% were taken for the calculation of total impurities.
1H NMR:
[00345] Bruker DPX 300 using a frequency of 300.13 MHz, a 30° excitation pulse and a recycle delay of 1 s. 16-1024 scans were accumulated per spectrum; deuterated DMSO or D2O was used as a solvent. Two-dimensional COSY spectra were acquired with 512 data points in the indirect dimension, an indirect time increment of 441.60 µs, 16 scans per slice and a recycle delay of 0.36 s. Differential Scanning Calorimetry (DSC):
[00346] DSC was performed using a TA Q200/Q2000DSC from TA Instruments using a ramp method and a crimped, aluminum sample pan at 25 °C. The heating rate was 10 °C/minute, and the purge gas was nitrogen.
EXAMPLE 1
POLYMORPH SYNTHESIS
Figure imgf000082_0001
Scheme 1. [00347] Step 1: A-1 was treated with boron tribromide in chlorobenzene. Removal of byproducts by distillation and crystallization from chlorobenzene-methanol-water resulted in A-2 as free base.
[00348] Step 2: A-2 (in free base form) was treated with diethyl chlorophosphate and diisopropylethylamine in N-methylpyrrolidone. Water was added to stop the reaction and precipitate the product. The resulting slurry was filtered, washed with water, and dried under vacuum to produce the compound A-3.
[00349] Step 3: A-3 was treated with trimethylsilyl bromide to deprotect A-3 and afford A-4 as a hydrobromide, which was treated with ammonium bicarbonate solution. The precipitated A-4 (i.e., compound of structure (I) having an amorphous crystal structure (i.e., "Form A") was filtered and dried.
[00350] Step 4: A-4 was suspended in a mixture of THF and water (19:1), and maleic acid was added. After stirring at room temperature, the solid was filtered and dried in a filter dryer to afford A-5. The resultant filtered solid compound A-5 was suspended in ethanol and re-slurried before an additional filtration. Filtered product (i.e., A-5 as polymorph form B) was washed with ethanol and dried to afford the desired product.
[00351] Synthesis of polymorph Form B according to Scheme 1 has been conducted using 5.72 kg A-1, 4.17 kg A-2 and 2.70 kg A-3. At this scale, the yield of Step 1 was 79.9%. After recrystallization, the yield of A-3 from Step 2 was 48%, and the purity of compound A-3 thus obtained was 86% by HPLC. The combined yield of Steps 3 and 4 was 37.5%. The overall yield of the process of Scheme 1 was 15%, and the process yielded 0.90 kg of A-5.
EXAMPLE 2
STABILITY STUDY
[00352] Initial attempts to isolate the compound of structure (I) produced an amorphous form, designated "Form A." Form A showed poor stability, decomposing to compound A-2. The results of a DVS (dynamic vapor sorption) test of Form A showed that the compound was hygroscopic, taking in 12.5% of its weight of water at 80% relative humidity. After 10 days at room temperature, Form A showed 6.85% degradation to compound A-2. [00353] The decomposition exhibited a strong temperature dependence. Samples stored at -20 °C showed no degradant trends, but a stability test of Form A at 40 °C and 75% relative humidity for one week showed accelerated decomposition. The DSC and TGA plots of Form A exhibited the characteristics predicted by hydrolytic
decomposition, as shown in FIG.2.
EXAMPLE 3
SALT SCREENING STUDY
[00354] A total of eight lattice/salt forming reagents (5 acids and 3 bases) and four solvent systems were selected for salt screening. Screening conditions are outline below in Table 1:
Figure imgf000085_0001
* the molar ratio of freebase and lattice forming reagent is 1:1.
** purity decrease (5~14 area%) was observed from HPLC results.
[00355] When the compound of structure (I) was crystallized together with maleic acid or L-tartaric acid in aqueous THF, the resulting crystal showed identical polymorph to Form B, indicating structure (I) does not form a salt with those acids. Although some amount of acid will remain in the isolated crystal with above recrystallization process for obtaining Form B, it was discovered that residual maleic acid could be removed via a re-slurry in ethanol. In contrast, the tartaric acid did not readily wash from the compound via the ethanol slurry. EXAMPLE 4
SALT SCREENING STUDY
[00356] Two larger scale pilot batches were synthesized according to the process described above in Example 1 to confirm and optimize the process. The results of these batches are shown in Tables 2, 3, and 4, below.
Figure imgf000086_0001
[00357] After removing the maleic acid from the polymorph of Form B (A-5) via a re-slurry in ethanol, the resultant polymorph was dried by a flow of nitrogen on a filter to reduce water to below 0.5%. Re-slurrying in ethanol does not increase the
concentration of impurity (A-2) in the slurry. Without wishing to be bound by theory, it is thought that the formation of compound A-2 is sensitive to water included in the crystal/polymorph form after formation. That is, when water content kept low enough following polymorph formation, hydrolysis of the phosphate moiety is prevented but the lattice forming reagent (e.g., maleic acid) can be removed. EXAMPLE 5
STABILITY STUDY
[00358] A stability study of the polymorph of the compound of structure (I) (compound A-5) with low water content sample (0.38%) showed a pronounced improvement in the compound stability (Table 5), indicating improved stability of the polymorph having the lower water content.
Figure imgf000087_0001
[00359] Based on this information, it can be concluded that the polymorph of the compound of structure (I) ("Form B") formed via a THF/water polymorph
transformation with maleic acid, followed by ethanol re-slurry to remove the residual maleic acid and water from the polymorph provides an unexpectedly stable compound.
EXAMPLE 5
ADDITIONAL POLYMORPH FORMATION STUDIES– POWDER X-RAY DIFFRACTION
[00360] During preliminary salt co-crystal screening (Example 3, above), it became apparent that nearly identical polymorphs were being formed despite the use of different acids or co-crystal screening agents. This is illustrated in FIG.3, which shows maleic and nicotinic acids along with D-xylose screening studies. This experiment provided evidence that these lattice forming reagents were not forming salts or co- crystals with the compound of structure (I), but were actually forming a polymorph (i.e., Form B) having the XRPD diffractogram shown in FIG.1. EXAMPLE 6
SINGLE CRYSTAL X-RAY DIFFRACTION
[00361] The absolute stereochemistry, the position of the phosphoric acid moiety, as well as the zwitterionic nature of the polymorph of the compound of structure (I) (Form B) were determined by a single crystal X-ray diffraction. Single crystal X-ray diffraction of Form B is shown in FIG.4. Form B crystallizes as an anhydrous molecule without solvent inclusion. Bond distances and angles are all within the expected values. EXAMPLE 7
FORMATION OF POLYMORPH FORM C
[00362] Two experimental conditions were explored for forming a new solid form of a compound of structure (I). A solvent mixture of acetone/water and ethanol/water were added to Form A. The experimental condition including acetone/water as the solvent was successfully reproduced on a larger scale. The diffractograms of the resultant solid form ("Form C") are shown in FIG.5. Although the diffractograms indicate the resultant product is highly crystalline, a TG-FTIR thermogram (FIG.6A) indicated Form C was associated with a significant amount of water. As evidenced by the thermogram, some solvent is released below the boiling point of water, but a large percentage appears to be tightly bound, which indicates that the sample is highly hydrated.
[00363] In order to determine whether Form C was stable with respect to
dehydration, a sample of Form C was dried under vacuum at 40 °C for about 24 hours. After drying, the sample contained about 5.4 weight percent water, which was close to the 5.3 weight percent theoretically expected for a sesquihydrate (see FIG.6B).
However, this sample lost significant crystallinity upon drying, so it is not necessarily a stoichiometric hydrate. Form C was found not to be stable to drying conditions with the resultant product being poorly crystalline.
[00364] The 1H NMR spectra of the three different forms (A, B and C) are distinguishable. All samples were recorded in DMSO-d6. The chemical shifts of the amorphous Form A and the Form C sample are substantially identical to each other but differ from those of Form B (FIG.7). The position of the proton near 7 ppm is markedly different for the spectrum of Form B, as is the presence of the peak near 12.8 ppm for Form B (i.e., which is absent in Forms A and C). EXAMPLE 8
POWDER X-RAY DIFFRACTION SPECTRUM
[00365] Polymorph Form B was analyzed using XRPD using the parameters described above. The resultant diffractogram is shown in FIG.1. Tabulated data generated for Form B is shown in Table 6, below:
Figure imgf000089_0001
Figure imgf000090_0001
EXAMPLE 9
FORMULATION STABILITY STUDY
[00366] Polymorph Form B (API) was formulated into two blends for four-week stability studies. Four excipients were tested in the following mixtures:
[00367] Binary mixtures (16 mg) 1. 11.43% API + 87.57% DCP anhydrous + 1% Magnesium stearate 2. 11.03% API + 87.97% Lactose anhydrous + 1% Magnesium stearate 3. 22.86% API + 76.14% Avicel PH200 LM + 1% Magnesium stearate 4. 17.78% API + 80.22% Mannitol 200 SD + 1% Magnesium stearate + 1% Aerosil 200
[00368] Binary mixtures (1 mg) 1. 0.50% API + 97.50% DCP anhydrous + 1% Magnesium stearate + 1% Aerosil 200
2. 0.53% API + 97.47% Lactose anhydrous + 1% Magnesium stearate + 1% Aerosil 200
3. 1.18% API + 97.82% Avicel PH200 LM + 1% Magnesium stearate 4. 0.91% API + 97.09% Mannitol 200 SD + 1% Magnesium stearate + 1% Aerosil 200
[00369] The appearance results for the study performed at 20 °C and 60% relative humidity (RH) and the study performed at 40 °C and 75% RH are shown in Table 7. The initial related substance results are shown in Table 8. The related substance results after two weeks at 25 ºC and 60% RH are shown in Table 9, and after four weeks at 25 ºC and 60% RH are shown in Table 10. The related substance results after two weeks at 40 °C and 75% RH are shown in Table 11, and after four weeks at 40 °C and 75% RH are shown in Table 12. The content uniformity for each batch of 16 mg capsules is shown in Table 13. The content uniformity for each batch of 1 mg capsules is shown in Table 14. Table 7.
Figure imgf000092_0001
Table 8.
Figure imgf000093_0001
Table 9.
Figure imgf000093_0002
Table 10.
Figure imgf000094_0001
Table 11.
Figure imgf000094_0002
Table 12.
Figure imgf000095_0001
Table 13.
Figure imgf000095_0002
Figure imgf000096_0002
EXAMPLE 10
Figure imgf000096_0001
Scheme 2. [00370] Step 1.1: To a clean and dry, three-necked, round-bottomed flask (RBF) (3 L) was added A-1 (90 g, 0.192 mol) and chlorobenzene (774 ml) at room temperature. To the reaction flask was slowly added BBr3 (391.5 g) at room temperature. After completion of BBr3 addition, the temperature of the reaction mixture was slowly raised to 80-83 °C, and the reaction mixture was stirred at the same temperature for 10 hours. The reaction mixture temperature was further raised to 100-103 °C, and the reaction mixture was maintained at 100-103 °C for 5 hours. The reaction progress was monitored by TLC and HPLC. After completion of the reaction, HBr and methyl bromide was removed at room temperature by nitrogen bubbling into the reaction mixture, while maintaining the vigorous stirring. The reaction mixture was slowly quenched with a mixture of methanol (180ml)/water (90ml) (270 ml), followed by methanol (180 ml). The solvent was removed under atmospheric distillation at 25-50 °C to reach the target reaction mass volume of 12 volumes (vol). Then, the reaction mixture pH was adjusted to 3.0 ± 1 using sodium hydroxide solution (48.8 g dissolved in 135 ml of DM water) at 50-55 °C. Again, the solvent was removed under
atmospheric distillation at 50-100 °C to reach the target reaction volume of 12 vol. Then, the pH of the reaction mixture was adjusted to pH 8.1 ± 0.2 using sodium hydroxide solution (8.5 g dissolved in 87 ml of DM water) at 50 °C followed by slow addition of water with constant stirring at 50 °C for 1 hour. The reaction mixture was slowly allowed to come to room temperature and maintained at room temperature for 3 hours. The resulting solid was filtered and washed with a mixture of methanol (315 ml)/water (135 ml) (3 x 450 ml) followed by water (5 x 450 ml). The solid was dried in a vacuum oven at 50-55 °C for 48 hours to obtain A-2 as a yellow solid (70 g, 90%). HPLC Purity: 99.72%.
[00371] Step 2.1A: To a clean and dry, three-necked RBF (3 L) was added A-2 (35.0 g, 0.087 mol) and DMF (245 ml), at room temperature, under nitrogen atmosphere. Then, DMAP (1.06 g, 0.0086 mol) followed by CCl4 (66.5 g 0.434mol) were added to the reaction mixture at room temperature. To the reaction mixture di-tertiary butyl phosphite (25.5g, 0.131 mol) was added at room temperature. The reaction mixture was stirred at room temperature under nitrogen atmosphere for 24 hours. The reaction progress was monitored by HPLC. The reaction mixture was cooled to 0-5 °C, and was quenched with slow addition of DM water (1950 ml) for 30 minutes at 0-5 °C. Then, chloroform (1627.5 ml) was added to the reaction mixture, and the reaction mixture was stirred at 0-5 °C for 10 minutes. The organic layer was separated and dried over sodium sulfate. The solvent was removed under reduced pressure, while maintaining the bath temperature below 45 °C. The resulting residue was co-distilled with toluene (4 × 175 ml). The residue was kept under high vacuum for 45 minutes to obtain A-10 as a pale yellow residue. (51.0 g, 98.5%). HPLC Purity: 91.48%.
[00372] Step 2.1B: To a clean and dry RBF (1 L) was added A-10 (51.0 g, 0.0858 mol) and acetic acid (102 ml) at room temperature. Then, 4N HCl solution in 1,4- dioxane (102 ml) was added dropwise at 25-30 °C. The reaction mixture was stirred at 25-30 °C for 40 minutes. The reaction progress was monitored by TLC. After completion of the reaction, toluene (2 × 510 ml) was added to the reaction mixture under stirring, and the reaction mixture was maintained for 5 minutes. The stirring was stopped, and the solids in the reaction mixture were allowed to settle at 25-30 °C for 5 minutes. The solvent was decanted to obtain the semi-solid. The semi-solid was co- distilled with toluene (3 x 123 ml) to obtain pale yellow solid. The resulting pale yellow solid was taken into a clean RBF, and methanol was added (123 ml) followed by dropwise addition of water (41 ml) at 25-30 °C. The reaction mixture was stirred at 25- 30 °C for 2 hours to obtain pale yellow solid. The resulting solid was filtered and vacuum dried for 10 minutes to obtain A-11 as a pale yellow solid (36.5 g, 82%). HPLC Purity: 97.03%. This material was directly taken into Step 3.1 without further drying.
[00373] Step 3.1: To a clean and dry, three-necked, 500 ml RBF was added A-11 (34.0 g, 0.066 mol) and ACN (51 ml). To the reaction mixture was dropwise added ammonium bicarbonate solution (16.2 g dissolved in 170 ml of DM water) under stirring at 25-30 °C for 30 minutes. Again, ACN (51 ml) was slowly added at 25-30 °C for 30 minutes. The reaction mixture was cooled to 10-15 °C and stirred at 10-15 °C for 60 minutes. The resulting solid was filtered and washed with ACN (102 ml). The solid was dried in a vacuum oven at 25-30 °C for 16 hours to obtain A-4 as a pale yellow solid (28.5 g, 90.10%). HPLC Purity: 99.68%.
[00374] Step 4.1: To a clean and dry, 500-ml, three-necked RBF was added A-4 (7.5 g, 0.015 mol) and methanol (187.5 ml) at room temperature. To the reaction mixture was slowly added acetic acid (7.5 ml, 1.0 vol) at 50 °C, under nitrogen atmosphere. The reaction mixture was stirred at 50 °C for 1 h, under nitrogen atmosphere. The reaction mixture was cooled to room temperature and stirred for 2 h. The solid was filtered and dried under vacuum to obtain 5.0 g A-5 (66.5%) as a pale yellow solid. HPLC Purity: 99.77%.
[00375] Several screens were conducted to identify the Step 4.1 conditions described above. In a first screen, A-4 was treated with acid (1.0 volume) and methanol (25 volumes) according to the conditions listed in Table 15 to obtain A-5 as a pale yellow solid.
Figure imgf000099_0001
Figure imgf000100_0002
[00376] In another screen, A-4 was treated with acetic acid (1 volume) and a solvent (25 volumes) according to the conditions listed in Table 16 to obtain A-5 as a pale yellow solid.
Figure imgf000100_0001
Figure imgf000101_0001
[00377] In another screen, A-4 was treated with acetic acid (1 volume) and a solvent according to the conditions listed in Table 17 to obtain A-5 as a pale yellow solid. Table 17.
Figure imgf000101_0002
Figure imgf000102_0001
Figure imgf000103_0002
[00379] As an alternative to conducting Step 4.1 using the conditions cited above in Example 10, a procedure similar to that described in Step 4 of Example 1 can be used to effect polymorph conversion. Thus, in another experiment, to a clean and dry, 100-ml, three-necked RBF was added A-4 (2.0 g, 0.004 mol), THF (29 ml) and DM water (1.7 ml) at room temperature. Then, maleic acid (0.44 g) was added to the reaction mixture at room temperature. The reaction mixture was stirred at room temperature for 12 h. The resulting solid was filtered and vacuum dried. The wet solid was dissolved in ethanol (12 ml) at room temperature and was stirred for 24 h. The resulting solid was filtered, washed with ethanol (2.5 ml), vacuum dried to obtain A-5 (1.5g, 60%) as a pale yellow solid. HPLC Purity: 99.91%. EXAMPLE 11
FORMULATION STABILITY STUDY
[00380] Polymorph Form B obtained using various Step 2.1B reaction conditions was submitted to a four-week stability study. The results of the stability study appear in Table 19. The Reference Standard is a sample obtained using the synthetic procedure described in Example 1.
Figure imgf000103_0001
Figure imgf000104_0001
[00381] Polymorph Form B obtained using the Step 2.1B reaction conditions described in Scheme 2 was submitted to a four-week stability study to test the effects of different packing conditions on the stability of A-5. Under Packing Condition 1, polymorph Form B was packed into an amber-colored bottle, which was closed with a rubber stopper and sealed with a flip-off aluminum cap. Under Packing Condition 2, polymorph Form B was packed in a low-density polyethylene bag (LDPE) twisted and tied. The LDPE bag was then inserted into a black, LDPE bag along with one silica gel bag, and the black, LDPE bag was heat sealed under nitrogen atmosphere. The black, LDPE bag was then inserted into a triple-laminated aluminum bag along with one silica gel bag, and the aluminum bag was heat sealed under nitrogen atmosphere. The triple- laminated aluminum bag containing polymorph Form B was kept in a high-density polyethylene container. The results of the stability study appear in Table 20. Table 20.
Figure imgf000104_0002
EXAMPLE 12
FORMULATION STABILITY STUDY [00382] Polymorph Form B obtained using various Step 4.1 reaction conditions described in Example 10 was submitted to a four-week stability study. The results of the stability study appear in Table 21. Table 21.
Figure imgf000105_0002
EXAMPLE 13
EXCIPIENT COMPATIBILITY STUDY [00383] The compatibility of binary mixtures of 95% excipient and 5% compound of structure (I) (equivalent to a 20:1 excipient:compound of structure (I) ratio) was studied. The following excipients formed part of the excipient compatibility study:
Figure imgf000105_0001
Figure imgf000106_0002
[00384] Samples were tested for related substances (Total Impurities, by HPLC) at 50 °C and 85% RH, and at 60 °C at two- and four-week time points. Anhydrous lactose, cornstarch, partly pregelatinized starch, low-substituted hydroxyl propyl cellulose, carmellose calcium and magnesium stearate demonstrated compatibility with the compound of structure (I). The results of the excipient compatibility study are described in Tables 22A-22P.
Figure imgf000106_0001
Figure imgf000107_0001
Figure imgf000108_0001
Figure imgf000109_0001
Figure imgf000110_0001
Figure imgf000111_0001
Figure imgf000112_0001
Figure imgf000113_0001
Figure imgf000114_0001
Figure imgf000115_0001
Figure imgf000116_0001
[00385] Samples were also tested for dissolution. Six capsules were tested for dissolution according to the parameters outlined in Table 23. Each capsule was weighed prior to dissolution testing. The stated amount of dissolution medium was transferred into each vessel in accordance with the capsule strength under analysis. The dissolution medium was allowed to equilibrate in the dissolution bath to 37 °C ± 0.5 °C. The temperature of the dissolution medium checked at the start and end of the dissolution test for each vessel. At each sample point, the solution was transferred directly into an HPLC vial.
Table 23. Dissolution Conditions
Figure imgf000117_0002
[00386] The following calculations were used to calculate the sample concentration, amount released and percent released, respectively. P811 corresponds to the compound of structure (I).
Figure imgf000117_0001
Figure imgf000118_0001
[00387] The results of the dissolution testing are shown in FIGs.9A-9D.
EXAMPLE 14
FORMULATIONS OF COMPOUND OF STRUCTURE (I) AND STABILITIES THEREOF
[00388] The following mixtures of the compound of structure (I) were formulated into 1-mg strength capsules, wherein the percentages are calculated on a weight/weight basis:
Figure imgf000118_0002
Figure imgf000119_0003
[00389] The following mixture of the compound of structure (I) was formulated into a 4-mg strength capsule, wherein the percentages are calculated on a weight/weight basis:
Figure imgf000119_0002
[00390] The following mixtures of the compound of structure (I) were formulated into 16-mg strength capsules, wherein the percentages are calculated on a
weight/weight basis:
Figure imgf000119_0001
[00391] For manufacturing, a powder blend of compound of structure (I) and the indicated excipients were encapsulated into #4 hydroxypropylmethylcellulose (HPMC) capsules. The resulting capsules were immediate-release capsules.
[00392] Prior to encapsulation into the capsules, the drug product was made by direct blending via triturating the compound of structure (I) into the indicated excipients, followed by filling the capsules on a manual capsule filling machine in 100-capsule plates.
[00393] The capsules were packaged in aluminum blister packaging, with one capsule per blister and seven capsules per blister sheet. Three blisters on each sheet were left empty.
[00394] One-month stability testing of the compositions of the compound of structure (I) was performed at 40 °C and 75% RH, 25 °C and 60% RH or 5 °C. The compositions were tested for HPLC purity, impurities and dissolution. Tables 24-1 to 24-8 report the results of the impurity testing, and show that cornstarch-based formulations improved capsule stability compared to Formulation Nos.401-01 and 401- 06. Tables 25-1 to 25-8 report the results of the HPLC purity assay. FIGs.10A to 10X show the results of the dissolution testing conducted according to the dissolution procedure described in Example 13. All of the formulations submitted to dissolution testing met the criteria of Q (compound of structure (I)) = 75% within 45 minutes.
Figure imgf000120_0001
Figure imgf000121_0001
Figure imgf000122_0001
Figure imgf000123_0001
Figure imgf000124_0001
EXAMPLE 15
PHASE I, PHARMACOKINETIC (PK) AND PHARMACODYNAMIC (PD), DOSE-ESCALATION STUDY OF ORAL COMPOUND OF STRUCTURE (I) ADMINISTERED TO PATIENTS WITH
ADVANCED SOLID TUMORS
[00395] Patients with advanced metastatic or progressive solid tumors who were refractory to, or intolerant of, established therapy known to provide clinical benefit for their condition were enrolled. Cohorts of 3-6 patients each received escalating doses of compound of structure (I) using a modified Fibonacci dose escalation approach. Once the optimal dose has been established, additional patients may be enrolled to confirm safety and to explore efficacy.
[00396] This is an ongoing Phase 1, open-label, dose-escalation, safety, PK and PD study. The proposed starting dose and schedule for oral compound of structure (I) was a 1-mg flat dose once daily (QD) for 14 days followed by a 7-day drug-free recovery period (each cycle = 21 days). In the absence of dose-limiting toxicities (DLTs) in the first cohort of at least 3 patients, the dose was increased using a modified Fibonacci dose escalation scheme, and BID dosing commenced according to the dose escalation schedule described in Table 28. The first patient in cohort 6 has been enrolled at 8 mg compound of structure (I) BID. The baseline demographics of the first 14 patients enrolled in the study are described in Table 26. Table 26. Baseline Demographics (N = 14 ITT)
Figure imgf000125_0002
[00397] FIG.12 is a graph depicting completed cycles on the study through Cohort 5.
[00398] To date, there is no unexplained toxicity, and no evidence of dose-limiting diarrhea or neutropenia. The treatment-emergent adverse events of grade ³ 3 observed thus far are reported in Table 27. Table 27. Treatment-emergent adverse events grade ³ 3.
Figure imgf000125_0001
[00399] Sequential cohorts of 3 patients will continue to be treated with escalating doses according to Table 28 until the MTD is established.
Figure imgf000126_0001
[00400] If a DLT is observed in 1 of 3 patients at a given dose level, up to
3 additional patients will be enrolled and treated at that dose level. When up to 3 additional patients are added to a given dose level, if only 1 out of those 6 patients experiences a DLT, the dose will be increased to the next dose level. If ³2 out of 3-6 patients at a dose level experience DLTs, the dose will be decreased to the previous (lower) dose level and 3 additional patients will be enrolled at that dose level.
[00401] If 0 or 1 patient in any of the 6 patients experience a DLT, but the next higher dose level has already been studied, then the current dose will be declared the MTD and the study will advance to the expansion cohort.
[00402] The MTD is defined as the dose at which £1 of 6 patients experience a DLT during Cycle 1 with the next higher dose having at least 2 of 3 to 6 patients experiencing a DLT during Cycle 1.
[00403] Once the MTD has been established, 20 additional patients will be enrolled at the MTD. Data collected from patients enrolled at the MTD will be used to confirm safety, explore potential biomarkers, and evaluate potential signals of compound of structure (I) activity.
[00404] All patients may continue to receive compound of structure (I) in 21-day cycles (14 days of active treatment) at the same dose given during Cycle 1 until they experience unacceptable toxicity or unequivocal disease progression. No intra-patient escalation of the compound of structure (I) dose is permitted during the escalation phase until MTD is established.
[00405] Patients met all of the following inclusion criteria:
1. Have a histologically confirmed diagnosis of advanced metastatic or progressive solid tumor excluding tumor types with rapid cell turnover, i.e., small cell cancer (lung and extra pulmonary), inflammatory breast cancer (IBC), medulloblastoma, neuroblastoma and melanoma with extensive liver metastasis (³50% of the liver involved; patients with melanoma and metastasis to <50% of the liver were eligible)
2. Be refractory to, or intolerant of, established therapy known to provide clinical benefit for their condition
3. Have one or more tumors measurable or evaluable as outlined by the Response Evaluation Criteria in Solid Tumors (RECIST) v1.1
4. Have an Eastern Cooperative Oncology Group (ECOG) performance status of £1
5. Have a life expectancy ³3 months
6. Be ³18 years of age
7. Have a negative pregnancy test (if female of childbearing potential)
8. Have acceptable liver function:
a) Bilirubin £1.5x upper limit of normal (ULN) (unless associated with Gilbert syndrome)
b) Aspartate aminotransferase (AST/SGOT), alanine aminotransferase (ALT/SGPT) and alkaline phosphatase £2.5x ULN*
* if liver metastases were present, then 3x ULN was allowed 9. Have acceptable renal function: calculated creatinine clearance ³30 mL/min 10. Have acceptable hematologic status:
c) Granulocyte ³1500 cells/mm3
d) Platelet count ³100,000 (plt/mm3)
e) Hemoglobin ³8 g/dL
11. Have acceptable coagulation status:
f) Prothrombin time (PT) within 1.5x normal limits g) Activated partial thromboplastin time (aPTT) within 1.5x normal limits 12. Be nonfertile or agree to use an adequate method of contraception. Sexually active patients and their partners used an effective method of contraception (hormonal or barrier method of birth control; or abstinence) prior to study entry and for the duration of study participation and for at least 3 months (males) and 6 months (females) after the last study drug dose.
13. Have read and signed the Institutional Review Board (IRB)-approved informed consent form (ICF) prior to any study-related procedure.
[00406] Patients meeting any one of the following exclusions criteria were prohibited from participating in the study:
1. History of congestive heart failure (CHF); cardiac disease, myocardial infarction within the past 6 months prior to Cycle 1/Day 1; left ventricular ejection fraction (LVEF) <45% by echocardiogram (ECHO), unstable arrhythmia, or evidence of ischemia on electrocardiogram (ECG) within 14 days prior to Cycle 1/Day 1 2. Have a corrected QT interval (using Fridericia’s correction formula) (QTcF) of >450 msec in men and >470 msec in women
3. Have a seizure disorder requiring anticonvulsant therapy
4. Presence of symptomatic central nervous system metastatic disease or disease that requires local therapy such as radiotherapy, surgery, or increasing dose of steroids within the prior 2 weeks
5. Have severe chronic obstructive pulmonary disease with hypoxemia (defined as resting O2 saturation of £90% breathing room air)
6. Have undergone major surgery within 2 weeks prior to Cycle 1/Day 1
7. Have active, uncontrolled bacterial, viral, or fungal infections, requiring
systemic therapy
8. Are pregnant or nursing
9. Received treatment with radiation therapy, surgery, chemotherapy, or
investigational therapy within 28 days or 5 half-lives, whichever occurs first, prior to study entry (6 weeks for nitrosoureas or mitomycin C)
10. Are unwilling or unable to comply with procedures required in this protocol 11. Have known infection with human immunodeficiency virus, hepatitis B, or hepatitis C. Patients with history of chronic hepatitis that is currently not active are eligible
12. Have a serious nonmalignant disease (eg, hydronephrosis, liver failure, or other conditions) that could compromise protocol objectives in the opinion of the Investigator and/or the Sponsor
13. Are currently receiving any other investigational agent
14. Have exhibited allergic reactions to a similar structural compound, biological agent, or formulation
15. Have malabsorption conditions (e.g., Crohn’s disease) or have undergone
significant surgery to the gastrointestinal tract that could impair absorption or that could result in short bowel syndrome with diarrhea due to malabsorption.
DLT was defined as any one of the following events observed in cycle 1, regardless of investigator attribution, unless there was a clear alternative explanation:
1. Grade 3 or greater febrile neutropenia
2. Grade 4 neutropenia for ³7 consecutive days
3. Grade 4 thrombocytopenia or Grade 3 thrombocytopenia with clinically
significant bleeding or that requires a platelet transfusion
4. Grade 3 or 4 nonhematologic AEs will be considered dose limiting, regardless of duration aside from the specific parameters described herein
5. Grade 4 nausea, vomiting, or diarrhea, regardless of duration
6. Dosing delays >1 week due to treatment-emergent adverse events (TEAEs) or related severe laboratory test values
7. Any AST and ALT elevation >3x ULN (if baseline value was normal) or ³3x the baseline value (if baseline value was abnormal) accompanied by serum bilirubin levels >2x ULN
8. Any Grade ³3 electrolyte disturbances (eg, hyperkalemia, hypophosphatemia, hyperuricemia) that do not resolve within <72 hours
9. Any Grade ³3 elevations in creatinine
10. Any Grade 5 toxicity
[00407] Plasma PK parameters of compound of structure (I) and alvocidib were evaluated in Cohorts 1-5 at specific timepoints during the study. Blood was collected from patients in Cohorts 1-5 according to the pharmacokinetic sampling schedule described in Table 29.
Figure imgf000130_0001
[00408] PK parameters were estimated using standard noncompartmental methods. Actual sample collection times were used rather than scheduled collection times.
Plasma concentrations below the limit of quantification were treated as 0. Imbedded missing plasma concentrations (e.g., missing values between two observed values) were estimated using linear extrapolation. This is consistent with using the trapezoidal rule to calculate AUC. Other missing plasma concentrations were excluded from calculations to estimate PK parameters.
[00409] FIGs.11A and 11B are graphs of plasma alvocidib concentration (ng/mL) versus time, and show the concentration of alvocidib in the plasma of patients in Cohort 1 on days 1 and 14, respectively, following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01. Subject 104 showed some accumulation of alvocidib after 24 hours on day 14. Subject 102 was discontinued prior to day 14 dosing.
[00410] FIGs.11C and 11D are graphs of plasma alvocidib concentration (ng/mL) versus time, and show the concentration of alvocidib in the plasma of patients in cohort 2 on days 1 and 14, respectively, following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01. Only alvocidib was detectable at 1 mg BID, and no compound of structure (I) was detected at any timepoint for any sample. No drug was detectable (less than 1.0 ng/mL of alvocidib) by 8 hours and again at 24 hours in any subject on day 1. However, there was detectable accumulation of alvocidib on day 14 for subjects 201 and 202 (average = 2.39 ng/mL), suggesting that BID dosing helped to maintain drug levels by day 14.
[00411] FIGs.11E and 11F are graphs of plasma alvocidib concentration (ng/mL) versus time, and show the concentration of alvocidib in the plasma of patients in Cohort 5 on days 1 and 14, respectively, following daily oral BID dosing with 6 mg of
Formulation No.401-01. Table 30 reports Tmax, Cmax and AUC(0-24) of alvocidib for patients in Cohort 5 on days 1 and 14 of cycle 1.
Table 30.
Figure imgf000131_0001
[00412] FIG. 11G is a graph of alvocidib (ng/mL) versus cohort, and shows the mean Cmax of alvocidib on day 1 and day 14 following daily oral QD dosing with a 1-mg strength capsule containing Formulation No.401-01. FIG.11H is a graph of alvocidib (ng*hr/mL) versus cohort, and shows the area under the curve (AUC) of alvocidib on day 1 (AUC0-8) and day 14 (AUC0-8 and AUC0-24) following daily oral BID dosing with a 1-mg strength capsule containing Formulation No.401-01. There was no detectable compound of structure (I) at any timepoint. Cohort 2 showed marked increase in average Cmax and AUC from day 1 to day 14, illustrating the impact of BID versus QD dosing. The Cmax for Cohort 5 increased by 46% compared to Cohort 4 on day 1, and by 69% for day 14. The corresponding increase in AUC was 52% on day 1 and 30% on day 14. [00413] FIG.11I is a graph of mean concentration of alvocidib (nM) versus time, and shows the mean concentration of alvocidib in plasma of Cohort 5 patients over a 24-hour period. By administering alvocidib as compound of structure (I), alvocidib can be given at a lower dose over a longer time, with less toxicity and similar exposure.
Figure imgf000132_0001
Scheme 3. [00414] A-10 was obtained according to Steps 1.1 and 2.1A, depicted in Scheme 2 and described in Example 10. A-10 (100 mg) was substantially dissolved in methanol (1 ml) at 50 °C. A solution of maleic acid (12.2 mg, 0.5 equiv) in methanol (1.5 ml) was added dropwise to the mixture of A-10 in methanol, followed by acetone (2.5 ml). The resulting reaction mixture was stirred for one hour at room temperature, and then filtered to obtain A-5 (77.4 mg) having a crystallinity of 94%. Residual maleic acid was confirmed by 1H NMR (0.01 proton).
EXAMPLE 17
A PHASE II STUDY OF ORAL COMPOUND OF STRUCTURE (I) ADMINISTERED ONCE DAILY FOR 21 DAYS TO PATIENTS WITH METASTATIC CASTRATE-RESISTANT PROSTATE
CANCER [00415] This is a Phase 2, open-label, non-randomized, Simon 2-stage design study to establish the efficacy and safety of compound of structure (I) (e.g., Form B of compound of structure (I)) taken once daily for 21 days of a 28-day cycle in patients with metastatic castration-resistant prostate cancer who have progressed on frontline treatment with androgen signaling inhibitors. A biopsy sub-study in 20 patients will enable the evaluation of tissue biomarkers in a subset of patients.
[00416] Sixty (60) patients will be enrolled. Data will be used to assess efficacy, confirm safety, and explore correlative potential biomarkers.
[00417] All patients may continue to receive compound of structure (I) in 28-day cycles (21 days of active treatment) at the same dose given during Cycle 1 until they experience unacceptable toxicity or unequivocal disease progression.
[00418] Patients must meet all of the following inclusion criteria to be eligible:
1. Male patients who also have histologically or cytologically confirmed
adenocarcinoma of the prostate; AND:
a) Be castrate-resistant on treatment with androgen deprivation therapy (ADT) (or status post bilateral orchiectomy) and with testosterone levels of less than (<) 50 nanogram per deciliter (50ng/dL, equivalent to 1.7 nmol/L); AND:
b) Have radiographic progression according to according to Prostate Cancer Clinical Trials Working Group 3 (PCWG3) criteria, while being treated with abiraterone acetate or enzalutamide in combination with ADT 2. Be refractory to, or intolerant of, established therapy known to provide clinical benefit for their condition
3. Have one or more tumors measurable as outlined by the Response Evaluation Criteria in Solid Tumors (RECIST) v1.1
4. Willingness to undergo two (2) on-study biopsies (biopsy sub-study cohort only) 5. Have an Eastern Cooperative Oncology Group (ECOG) performance status of £1
6. Have a life expectancy ³3 months
7. Be ³18 years of age
8. Have acceptable liver function:
a) Bilirubin £1.5x upper limit of normal (ULN) (unless associated with Gilbert syndrome) b) Aspartate aminotransferase (AST/SGOT), alanine aminotransferase (ALT/SGPT) and alkaline phosphatase £2.5x ULN*
*If liver metastases are present, then 3x ULN is allowed.
9. Have acceptable renal function: calculated creatinine clearance ³30 mL/min 10. Have acceptable hematologic status:
a) Granulocyte ³1500 cells/mm3
b) Platelet count ³100,000 (plt/mm3)
c) Hemoglobin ³8 g/dL
11. Have acceptable coagulation status:
a) Prothrombin time (PT) within 1.5x normal limits
b) Activated partial thromboplastin time (aPTT) within 1.5x normal limits 12. Be nonfertile or agree to use an adequate method of contraception. Sexually active patients and their partners must use an effective method of contraception (hormonal or barrier method of birth control; or abstinence) prior to study entry and for the duration of study participation and for at least 3 months (males) and 6 months (females) after the last study drug dose. Should a woman become pregnant or suspect she is pregnant while her partner is participating in this study, she should inform her treating physician immediately.
13. Have read and signed the Institutional Review Board (IRB)-approved informed consent form (ICF) prior to any study-related procedure. (In the event that the patient is rescreened for study participation or a protocol amendment alters the care of an ongoing patient, a new ICF must be signed.)
[00419] Patients meeting any one of these exclusion criteria will be prohibited from participating in this study:
1. History of congestive heart failure (CHF); cardiac disease, myocardial infarction within the past 6 months prior to Cycle 1/Day 1
2. Have a corrected QT interval (using Fridericia’s correction formula) (QTcF) of >450 msec in men and >470 msec in women
3. Have a seizure disorder requiring anticonvulsant therapy
4. Presence of symptomatic central nervous system metastatic disease or disease that requires local therapy such as radiotherapy, surgery, or increasing dose of steroids within the prior 2 weeks 5. Have severe chronic obstructive pulmonary disease with hypoxemia (defined as resting O2 saturation of £90% breathing room air)
6. Have undergone major surgery within 2 weeks prior to Cycle 1/Day 1
7. Have active, uncontrolled bacterial, viral, or fungal infections, requiring
systemic therapy
8. Are pregnant or nursing
9. Received treatment with radiation therapy, surgery, chemotherapy, or
investigational therapy within 28 days or 5 half-lives, whichever occurs first, prior to study entry (6 weeks for nitrosoureas or mitomycin C)
10. Are unwilling or unable to comply with procedures required in this protocol 11. Have known infection with human immunodeficiency virus, hepatitis B, or hepatitis C. Patients with history of chronic hepatitis that is currently not active are eligible
12. Have a serious nonmalignant disease (e.g., hydronephrosis, liver failure, or other conditions) that could compromise protocol objectives in the opinion of the Investigator and/or the Sponsor
13. Are currently receiving any other investigational agent
14. Have exhibited allergic reactions to a similar structural compound, biological agent, or formulation
15. Have malabsorption conditions (e.g., Crohn’s disease, etc.) or have undergone significant surgery to the gastrointestinal tract that could impair absorption or that could result in short bowel syndrome with diarrhea due to malabsorption.
[00420] Enrolled patients will receive compound of structure (I) (e.g., given as a 1- mg capsule containing Formulation No.401-01, wherein the compound of structure (I) is Form B of the compound of structure (I)), administered once daily (QD) for the first 21 days of a 28-day cycle. Patients who successfully complete a 4-week treatment cycle without evidence of significant treatment-related toxicity or progressive disease will continue to receive treatment with the same dose and dosing schedule.
[00421] Efficacy assessments will be performed based on PCWG3-modified
RECIST v1.1 guidelines, to include the assessment of objective response rate (ORR), DoR, type of response (e.g., complete remission, partial remission, stable disease), and time to progression. The ORR is defined as the percent of patients with CR or PR according to PCWG3-modified RECIST v1.1 criteria, relative to the Response
Evaluable population. ORR will be summarized by number and percentage of patients meeting the definition of ORR along with the corresponding exact 95% confidence intervals.
[00422] Tolerance and toxicity of oral compound of structure (I) will be assessed through evaluation of physical examinations, vital signs, laboratory parameters, AEs including DLTs, and all causes of mortality.
[00423] Incidence rates of treatment-emergent adverse events (TEAEs) will be summarized within each dose level at the Medical Dictionary for Regulatory Activities (MedDRA) preferred term and primary system organ class levels. Similar summaries will be made for subsets of AEs such as (1) those judged by the Investigator to be related to study treatment, and (2) serious adverse events (SAEs).
[00424] Other routine safety assessments (e.g., clinical laboratory parameters and vital signs) will be summarized by compound of structure (I) dose level using mean, standard deviation, median, minimum, and maximum changes from baseline values.
[00425] PD parameters and assessment of potential tumor and peripheral blood biomarkers including, but not limited to, CDK9-related genes (including c-Myc) in biopsy and CTC samples; Phospho-AR; PhosphoRNAPol2 on biopsy and PBMC samples; serum PSA.
[00426] Blood will be collected from all patients for evaluation of compound of structure (I) pharmacodynamics and potential biomarkers. Biopsy samples will be taken at baseline (prior to dosing on Cycle 1/Day 1) and at the end of cycle two (2) in a subset of patients participating in the biopsy sub-study.
[00427] The most recent archived tumor tissue (primary and metastatic site(s), if available) will be requested from all patients to assess potential biomarkers. [00428] All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification or the attached Application Data Sheet are incorporated herein by reference, in their entirety to the extent not inconsistent with the present description. [00429] From the foregoing it will be appreciated that, although specific embodiments of the disclosure have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the disclosure.

Claims

1. A crystalline form of a compound having the following structure (I):
Figure imgf000138_0001
or a tautomer or zwitterionic form thereof.
2. The crystalline form of claim 1, comprising Form B.
3. The crystalline form of claim 1, consisting essentially of Form B.
4. The crystalline form of claim 1, 2 or 3, wherein the crystalline form is
substantially pure.
5. The crystalline form of any one of claims 1-4, characterized by an x-ray powder diffraction pattern comprising at least three peaks at 2-theta angles selected from the group consisting of 4.8 ± 0.2°, 10.8 ± 0.2°, 13.7 ± 0.2°, 14.9 ± 0.2°, 20.0 ± 0.2° and 24.6 ± 0.2°.
6. The crystalline form of claim 5, characterized by an x-ray powder diffraction pattern comprising at least four peaks at 2-theta angles selected from the group consisting of 4.8 ± 0.2°, 10.8 ± 0.2°, 13.7 ± 0.2°, 14.9 ± 0.2°, 20.0 ± 0.2° and 24.6 ± 0.2°.
7. The crystalline form of claim 6, characterized by an x-ray powder diffraction pattern comprising at least five peaks at 2-theta angles selected from the group consisting of 4.8 ± 0.2°, 10.8 ± 0.2°, 13.7 ± 0.2°, 14.9 ± 0.2°, 20.0 ± 0.2° and 24.6 ± 0.2°.
8. The crystalline form of any one of claims 1-4, characterized by an x-ray powder diffraction pattern comprising peaks at the following 2-theta angles: 10.8 ± 0.2°, 14.9 ± 0.2° and 20.0 ± 0.2°.
9. The crystalline form of claim 8, characterized by an x-ray powder diffraction pattern comprising peaks at the following 2-theta angles: 4.8 ± 0.2°, 10.8 ± 0.2°, 14.9 ± 0.2° and 20.0 ± 0.2°.
10. The crystalline form of claim 9, characterized by an x-ray powder diffraction pattern comprising peaks at the following 2-theta angles: 4.8 ± 0.2°, 10.8 ± 0.2°, 13.7 ± 0.2°, 14.9 ± 0.2° and 20.0 ± 0.2°.
11. A crystalline form of a compound having the following structure (I):
Figure imgf000139_0001
or a tautomer or zwitterionic form thereof, having an x-ray powder diffraction pattern substantially in accordance with that depicted in FIG.1.
12. The crystalline form of any one of claims 1-11, characterized by a differential scanning calorimetry thermogram comprising an endothermic peak at about 264 °C.
13. The crystalline form of any one of claims 1-12, characterized by a differential scanning calorimetry thermogram substantially in accordance with that depicted in FIG.8.
14. The crystalline form of any one of claims 1-13, wherein the crystalline form is of a compound having structure (II):
Figure imgf000139_0002
15. A pharmaceutical composition comprising a crystalline form of any one of claims 1-14 and a pharmaceutically acceptable carrier or excipient.
16. The pharmaceutical composition of claim 15, formulated for oral administration.
17. The pharmaceutical composition of claim 15 or 16, in the form of a capsule.
18. The pharmaceutical composition of claim 15 or 16, in the form of a tablet.
19. The pharmaceutical composition of any one of claims 15-18, further comprising one or more additional therapeutic agents.
20. The pharmaceutical composition of any one of claims 15-19, provided in the form of a rapid release formulation.
21. The pharmaceutical composition of any one of claims 15-20, wherein the
pharmaceutically acceptable carrier or excipient is anhydrous lactose or cornstarch.
22. The pharmaceutical composition of any one of claims 15-21, further comprising a glidant.
23. The pharmaceutical composition of claim 22, wherein the glidant is colloidal silicon dioxide.
24. The pharmaceutical composition of any one of claims 15-23, further comprising a lubricant.
25. The pharmaceutical composition of claim 24, wherein the lubricant is
magnesium stearate.
26. The pharmaceutical composition of any one of claims 15-25, further comprising a disintegrant.
27. The pharmaceutical composition of claim 26, wherein the disintegrant is partly pregelatinized starch, low-substituted hydroxyl propyl cellulose or carmellose calcium.
28. A pharmaceutical composition comprising: from about 0.5 weight percent to about 11.25 weight percent of a compound having the following structure (I):
Figure imgf000141_0001
or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof; and from about 85 weight percent to about 99.5 weight percent of a
pharmaceutically acceptable carrier or excipient.
29. The pharmaceutical composition of claim 28, comprising from about 0.5 weight percent to about 1 weight percent of a compound having structure (I), or a tautomer or zwitterionic form thereof.
30. The pharmaceutical composition of claim 29, comprising about 1 mg of a
compound having structure (I), or a tautomer or zwitterionic form thereof.
31. The pharmaceutical composition of claim 28, comprising from about 10.5
weight percent to about 11.25 weight percent of a compound having structure (I), or a tautomer or zwitterionic form thereof.
32. The pharmaceutical composition of claim 31, comprising about 16 mg of a compound having structure (I), or a tautomer or zwitterionic form thereof.
33. The pharmaceutical composition of any one of claims 28-30, comprising from about 95 weight percent to about 99.5 weight percent of a pharmaceutically acceptable carrier or excipient.
34. The pharmaceutical composition of any one of claims 28-32, comprising from about 85 weight percent to about 90 weight percent of a pharmaceutically acceptable carrier or excipient.
35. The pharmaceutical composition of any one of claims 28-34, wherein the pharmaceutically acceptable carrier or excipient is anhydrous lactose or cornstarch.
36. The pharmaceutical composition of any one of claims 28-35, further comprising a glidant.
37. The pharmaceutical composition of claim 36, comprising about 1 weight percent of the glidant.
38. The pharmaceutical composition of claim 36 or 37, wherein the glidant is
colloidal silicon dioxide.
39. The pharmaceutical composition of any one of claims 28-38, further comprising a lubricant.
40. The pharmaceutical composition of claim 39, comprising about 1% of the
lubricant.
41. The pharmaceutical composition of claim 40, wherein the lubricant is
magnesium stearate.
42. The pharmaceutical composition of any one of claims 28-41, further comprising a disintegrant.
43. The pharmaceutical composition of claim 42, wherein the disintegrant is partly pregelatinized starch, low-substituted hydroxyl propyl cellulose or carmellose calcium.
44. A pharmaceutical composition comprising:
about 0.6 weight percent of a compound having the following structure (I):
,
Figure imgf000142_0001
or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof; about 97.4 weight percent of anhydrous lactose;
about 1 weight percent colloidal silicon dioxide; and
about 1 weight percent magnesium stearate.
45. A pharmaceutical composition comprising:
about 11 weight percent of a compound having the following structure (I):
Figure imgf000143_0001
or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof; about 87 weight percent of anhydrous lactose;
about 1 weight percent colloidal silicon dioxide; and
about 1 weight percent magnesium stearate.
46. A pharmaceutical composition comprising:
about 0.6 weight percent of a compound having the following structure (I):
Figure imgf000143_0002
or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof; and from about 98 weight percent to about 99.5 weight percent of cornstarch.
47. A pharmaceutical composition comprising: about 11 weight percent of a compound having the following structure (I):
Figure imgf000144_0001
or a tautomer, pharmaceutically acceptable salt or zwitterionic form thereof; and about 88 weight percent of cornstarch.
48. The pharmaceutical composition of claim 46 or 47, further comprising about 1 weight percent magnesium stearate.
49. The pharmaceutical composition of any one of claims 28-48, comprising the zwitterionic form of the compound having structure (I), the zwitterionic form having the following structure
Figure imgf000144_0002
50. The pharmaceutical composition of claim 49, comprising Form B.
51. A unit dose form comprising a pharmaceutical composition of any one of claims 15-50.
52. A method for treating a disease associated with overexpression of a cyclin- dependent kinase (CDK) in a mammal in need thereof, comprising
administering to the mammal a therapeutically effective amount of a crystalline form of any one of claims 1-14, or a pharmaceutical composition of any one of claims 15-50 or a unit dose form of claim 51.
53. The method of claim 52, wherein the disease is cancer.
54. The method of claim 53, wherein the cancer is a hematologic cancer.
55. The method of claim 54, wherein the hematologic cancer is selected from acute myelogenous leukemia (AML), follicular lymphoma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), multiple myeloma (MM), and non-Hodgkin’s lymphoma.
56. The method of claim 54, wherein the hematologic cancer is myelodysplasic syndrome (MDS).
57. The method of claim 53, wherein the cancer comprises a solid tumor.
58. The method of claim 53 or 57, wherein the cancer is bladder cancer.
59. The method of claim 53 or 57, wherein the cancer is lung cancer.
60. The method of claim 53 or 57, wherein the cancer is liver cancer.
61. The method of claim 53 or 57, wherein the cancer is prostate cancer.
62. The method of claim 53 or 57, wherein the cancer is a sarcoma.
63. The method of claim 53 or 57, wherein the cancer is renal cell carcinoma.
64. The method of any one of claims 53-63, wherein the cancer is c-Myc-altered.
65. The method of claim 64, wherein the cancer is lymphoma.
66. The method of claim 65, wherein the lymphoma is Burkitt lymphoma.
67. The method of claim 65, wherein the lymphoma is B-cell lymphoma or T-cell lymphoma.
68. The method of claim 64, wherein the cancer is cervical cancer, colon cancer, ovarian cancer, breast cancer, lung cancer, prostate cancer, colorectal cancer, pancreatic cancer, gastric cancer or uterine cancer.
69. The method of any one of claims 53-68, wherein the cancer is a primary cancer.
70. The method of any one of claims 53-69, wherein the cancer is a metastatic
cancer.
71. The method of any one of claims 52-70, wherein the crystalline form, the pharmaceutical composition or the unit dose form is administered orally.
72. A method for preparing crystalline Form B of a compound having the following structure (II):
Figure imgf000146_0001
the method comprising:
contacting amorphous compound having the following structure (I):
Figure imgf000146_0002
or a tautomer or zwitterionic form thereof, with an acid in a solvent, thereby preparing the crystalline Form B of the compound having structure (II).
73. The method of claim 72, wherein the acid has at least one pKa value that is less than about 5.
74. The method of claim 72 or 73, wherein the acid has a pKa value of greater than about 1.
75. The method of claim 72, 73 or 74, wherein the acid is an organic acid.
76. The method of claim 75, wherein the acid is selected from maleic acid, acetic acid, citric acid or propionic acid.
77. The method of claim 76, wherein the acid is maleic acid.
78. The method of claim any one of claims 72-77, wherein the solvent is tetrahydrofuran, methanol, ethanol, butanol, methyl ethyl ketone, acetone, diisopropylether, ethyl acetate or water, or a combination of any of the foregoing.
79. The method of any one of claims 72-78, wherein the solvent is an organic
solvent.
80. The method of any one of claims 72-79, wherein the solvent comprises
tetrahydrofuran.
81. A method for preparing crystalline Form B of a compound having the following structure (II):
Figure imgf000147_0001
the method comprising:
contacting a compound having the following structure (V):
Figure imgf000147_0002
or a tautomer, salt or zwitterionic form thereof, with an acid in a solvent, thereby preparing the crystalline Form B of the compound having structure (II).
82. The method of claim 81, wherein the acid has at least one pKa value that is less than about 5.
83. The method of claim 81 or 82, wherein the acid has a pKa value of greater than about 1.
84. The method of claim 81, 82 or 83, wherein the acid is an organic acid.
85. The method of claim 84, wherein the acid is maleic acid.
86. The method of claim any one of claims 81-85, wherein the solvent is
tetrahydrofuran, methanol, ethanol, butanol, methyl ethyl ketone, acetone, diisopropylether, ethyl acetate or water, or a combination of any of the foregoing.
87. The method of any one of claims 81-85, wherein the solvent is an organic solvent.
88. The method of any one of claims 81-87, wherein the solvent is a mixture of methanol and acetone.
89. The method of any one of claims 81-88, wherein the molar ratio of acid to compound having structure (V), or a tautomer or zwitterionic form thereof, is from about 0.4:1 to about 1.1:1.
90. The method of claim 89, wherein the molar ratio of acid to compound having structure (V), or a tautomer or zwitterionic form thereof, is about 0.5:1.
91. A method for preparing a compound having the following structure (I):
Figure imgf000148_0001
or a salt, tautomer or zwitterionic form thereof, the method comprising:
(a) contacting a compound having the following structure (IV):
Figure imgf000149_0001
or a tautomer or salt thereof, with di-tert-butylhalophosphonate in the presence of an amine base, thereby forming a compound having the following structure (V):
Figure imgf000149_0002
or a tautomer or salt thereof; and
(b) contacting the compound having structure (V), or a tautomer or salt thereof, with an acid,
thereby preparing a compound having structure (I), or a salt, tautomer or zwitterionic form thereof.
92. The method of claim 91, wherein the amine base is an organic amine base.
93. The method of claim 92, wherein the organic amine base is
diisopropylethylamine.
94. The method of claim 91, 92 or 93, further comprising contacting di-tert- butylphosphonate with carbon tetrahalide to prepare the di-tert- butylhalophosphonate.
95. The method of claim 94, wherein the di-tert-butylhalophosphonate is prepared in situ with the compound having structure (IV) by contacting di-tert- butylphosphonate with carbon tetrahalide.
96. The method of any one of claims 91-95, wherein the acid is hydrochloric acid or acetic acid, or a combination thereof.
97. The method of any one of claims 91-96, wherein the compound formed in step (b) is a salt of a compound having structure (I).
98. The method of claim 97, further comprising contacting the salt of a compound having structure (I) formed in step (b) with a base, thereby forming the compound having structure (I), or a tautomer or zwitterionic form thereof.
99. The method of claim 98, wherein the base is ammonium bicarbonate.
100. The method of any one of claims 91-95, wherein the acid is maleic acid.
101. The method of any one of claims 91-100, wherein the compound formed in step (b) is a compound having structure (II):
.
Figure imgf000150_0002
102. A method for preparing crystalline Form B of a compound having the following structure (II):
Figure imgf000150_0001
the method comprising:
(a) contacting a compound having the following structure (IV):
Figure imgf000151_0002
or a tautomer or salt thereof, with di-tert-butylhalophosphonate in the presence of an amine base, thereby forming a compound having the following structure (V):
Figure imgf000151_0003
or a tautomer or salt thereof; and
(b) contacting the compound having structure (V), or a tautomer or salt thereof, in an organic solvent, with an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1 in an organic solvent, thereby preparing crystalline Form B of a compound having structure (II).
103. A method for preparing crystalline Form B of a compound having the following structure (II):
Figure imgf000151_0001
the method comprising: (a) contacting a compound having the following structure (IV):
Figure imgf000152_0001
or a tautomer or salt thereof, with di-tert-butylhalophosphonate in the presence of an amine base, thereby forming a compound having the following structure (V):
Figure imgf000152_0002
or a tautomer or salt thereof;
(b) contacting the compound having structure (V), or a tautomer or salt thereof, with an acid having a pKa value of less than about 1, thereby forming a salt of a compound having the following structure (I):
Figure imgf000152_0003
(c) contacting the salt of a compound having structure (I) with a base, thereby forming amorphous compound having structure (I); and (d) contacting the amorphous compound having structure (I), in an organic solvent, with an acid having at least one pKa value that is less than about 5 and a pKa value of greater than about 1,
thereby preparing crystalline Form B of the compound having structure (II).
104. A combination comprising a crystalline form of any one of claims 1-14, and an additional therapeutic agent.
105. The combination of claim 104, further comprising a pharmaceutically
acceptable carrier or excipient.
106. The method of any one of claims 52-71, further comprising administering to the mammal an additional therapeutic agent.
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