Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
  • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
  • C07D487/04—Ortho-condensed systems
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
  • A61K31/4427—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems
  • A61K31/4439—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. omeprazole
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
• • 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
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
  • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings
• • 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
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
  • Y02P20/00—Technologies relating to chemical industry
  • Y02P20/50—Improvements relating to the production of bulk chemicals
  • Y02P20/55—Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Definitions

• ATR ATM and Rad3 related
• ATM and Rad3 related kinase is a protein kinase involved in cellular responses to DNA damage.
• ATR kinase acts with ATM ("ataxia telangiectasia mutated") kinase and many other proteins to regulate a cell's response to DNA damage, commonly referred to as the DNA Damage Response ("DDR").
• DDR DNA Damage Response
• the DDR stimulates DNA repair, promotes survival and stalls cell cycle progression by activating cell cycle checkpoints, which provide time for repair. Without the DDR, cells are much more sensitive to DNA damage and readily die from DNA lesions induced by endogenous cellular processes such as DNA replication or exogenous DNA damaging agents commonly used in cancer therapy.
• Healthy cells can rely on a host of different proteins for DNA repair including the DDR kinase ATR. In some cases these proteins can compensate for one another by activating functionally redundant DNA repair processes. On the contrary, many cancer cells harbour defects in some of their DNA repair processes, such as ATM signaling, and therefore display a greater reliance on their remaining intact DNA repair proteins which include ATR.
• ATR inhibitors may be useful for cancer treatment, either used alone or in combination with DNA damaging agents, because they shut down a DNA repair mechanism that is more important for cellular survival in many cancer cells than in healthy normal cells.
• ATR inhibitors may be effective both as single agents and as potent sensitizers to radiotherapy or genotoxic chemotherapy.
• ATR peptide can be expressed and isolated using a variety of methods known in the literature (see e.g., Unsal-Kacmaz et al, PNAS 99: 10, pp6673-6678, May 14, 2002; see also Kumagai et al. Cell 124, pp943-955, March 10, 2006; Unsal-Kacmaz et al. Molecular and
• FIGURE la XRPD Compound I-I anhydrous free base
• FIGURE 2a TGA Compound I-l anhydrous free base
• FIGURE 3a DSC Compound I-l anhydrous free base
• FIGURE lb XRPD Compound I-l hydrate
• FIGURE 2b TGA Compound I-l hydrate
• FIGURE 3b DSC Compound I-l hydrate
• FIGURE lc XRPD Compound I-l tartaric acid
• FIGURE 2c TGA Compound I-l tartaric acid
• FIGURE 3c DSC Compound I-l tartaric acid
• the present invention relates to solid forms of ATR inhibitors as well as deuterated ATR inhibitors.
• the present invention also relates to processes and intermediates for preparing an aminopyrazolopyrimidine compound useful as a potent inhibitor of ATR kinase.
• Amino-pyrazolopyrimidine derivatives are useful as ATR inhibitors and are also useful for preparing ATR inhibitors.
• One aspect of the invention provides a process for preparing compound I-l:
• Another aspect of the present invention comprises a compound of formula I-A:
• each Y , Y Y ⁇ Y Y , Y , and Y' is independently hydro gen or deuterium; provided at least one of Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 is deuterium; each X , X , and X is independently selected from C or C; and X 3 is independently selected from - 12 C(0)- or - 13 C(0)-.
• Another aspect of the present invention comprises a process for preparing a compound of formula I-l:
• Suitable conditions for forming the amide bond comprises reacting the compound of formula 6b with the substituted 3 -amino pyridine 11 in the presence of a solvent and an organic base.
• the solvent can be selected from NMP, DMF or anisole (preferred).
• the organic base is an aliphatic amine independently selected from triethylamine or DIPEA (preferred).
• Still other embodiments of the present invention comprises a process for preparing the compound of formula 11:
• Suitable metal catalysed cross-coupling conditions include a metal catalyst, a suitable solvent, and a suitable base.
• the metal catalyst is a palladium catalyst.
• suitable palladium catalysts include, but are not limited to,
• PdCl 2 (PPh 3 ) 2 , Pd(Ph 3 ) 4 , and PdCl 2 (dppf) (wherein each Ph is phenyl, and dppf is 1, 1- bis(diphenylphosphino)ferrocene).
• Suitable bases include, but are not limited to, potassium phosphate, K2CO3, tBuOK and a2C03.
• Suitable solvents include, but are not limited to, DME, tetrahydrofuran, toluene, and ethanol.
• Suitable deprotection conditions for removing the protecting group comprises reacting the protected species in the presence of a strong acid, such as HCl (preferred), HBr, sulfuric acid or trifluoroacetic acid.
• a strong acid such as HCl (preferred), HBr, sulfuric acid or trifluoroacetic acid.
• Another embodiment provides a process for preparing a compound of formula 9: by reacting the compound of formula 8:
• Suitable halogenation conditions comprises reacting compound 8 in an aprotic solvent, in the presence of a strong base, and an electrophilic source of halogen.
• the solvent can be selected from DCM, diethylether or THF (preferred).
• the strong base is selected from tert-BuLi, sec-BuLi or n-BuLi
• the electrophilic species used to introduce the halogen atom can, for example, be selected from I 2 (preferred), CF 3 I, diiodoethane, Br 2 , CBr 4 .
• Still other embodiments of the present invention provides a process for preparing a compound of formula 8:
• Suitable conditions for introducing the protecting group comprises reacting the amino species 7 in an aprotic solvent, in the presence of B0C 2 O. Such reaction can be conducted in the presence of a base.
• the solvent can be selected from diethylether or THF (preferred).
• the strong base can be selected from DMAP, n-BuLi, LHMDS or NaHMDS (preferred).
• Isotopes can be introduced on compound 1-1 by selecting building blocks that contain the isotopic atoms (either commercial or that can be prepared according to the literature) and engaging them into a sequence similar to the novel and inventive process reported for the unlabelled material (described above).
• Another aspect of the present invention provides a compound of Formula I-A:
• each Y , Y , Y Y Y , Y , and Y' is independently hydro gen or deuterium; provided at least one of Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 is deuterium; each X , X , and X is independently selected from C or C; and X 3 is independently selected from - 12 C(0)- or - 13 C(0)-.
• labelled building blocks which can be used in the synthetic route for preparing the compound of Formula I-A, are known to those skilled in the art. These may include, but are not limited to, the following labelled building blocks:
• Y 1 , Y 2 , Y 3 , and Y 4 are independently selected from deuterium or hydrogen; and Y 5 , Y 6 , and Y 7 are deuterium.
• Y 1 and Y 2 are independently selected from deuterium or hydrogen; and Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 are deuterium.
• Y 1 , Y 2 , Y 5 , Y 6 , and Y 7 are independently selected from deuterium or hydrogen; and Y 3 and Y 4 are deuterium.
• Y 1 , Y 3 , and Y 4 are independently selected from deuterium or hydrogen; and Y 2 , Y 5 , Y 6 , and Y 7 are deuterium.
• Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 are hydrogen; and X 4 is 13 C.
• Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 are hydrogen; and X 1 and X 4 are 13 C.
• Y 1 , Y 2 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 are hydrogen; and X 3 is - 13 C(0)-.
• Y , Y , Y , Y , Y , and Y are hydrogen; Y is deuterium; and X 4 is 13 C.
• Y , Y , Y , and Y are hydrogen; Y , Y , and Y are deuterium; and X 1 is 13 C.
• Y 1 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 are hydrogen; Y 2 is deuterium; and X 1 is 13 C.
• Y 1 , Y 2 , Y 3 , Y 5 , Y 6 , and Y 7 are hydrogen; Y 4 is deuterium; and X 1 is 13 C.
• Yl is hydrogen; Y 2 , Y 3 , Y 4 , Y 5 , Y 6 , and Y 7 are deuterium; X 2 is 13 C; and X 3 is - 13 C(0)-.
• the compounds of formula I-A of this invention are represented in Table 1. It will be appreciated by those skilled in the art that the compounds of the present invention may be represented in varying tautomeric forms. Table 1
• Another aspect of the present invention provides a solid form of a compound of formula 1-1 :
• the form is selected from the group consisting of Compound I-l anhydrous free base, Compound I-l hydrate, or Compound I-l tartaric acid .
• the solid form is Compound I-l anhydrous free base. In another aspect of the present invention, the solid form is crystalline Compound I-l anhydrous free base. In some embodiments, the solid form is characterized by one or more peaks expressed in 2-theta ⁇ 0.2 at about 9.9, 12.8, 15.4, 17.0, 23.1, 27.8, 29.0, and 30.1 degrees in an X-Ray powder diffraction pattern obtained using Cu K alpha radiation. In other embodiments, the solid form is characterized as having an X-ray powder diffraction pattern substantially the same as that shown in Figure la.
• the solid form is Compound I-l hydrate. In another aspect of the present invention, the solid form is crystalline Compound I-l hydrate. In other embodiments, the crystalline Compound I-l hydrate has a Compound I-l to water ratio of 1 :3. In still other embodiments, Compound I-l hydrate is characterized by a weight loss of from about 12.6% in a temperature range from about 40°C and about 100°C. In some embodiments, the solid form is characterized by one or more peaks expressed in 2- theta ⁇ 0.2 at about 27.5, 20.6, and 9.7 degrees in an X-Ray powder diffraction pattern obtained using Cu K alpha radiation. In yet other embodiments, the solid form is
• the solid form is Compound I-l tartaric acid.
• the solid form is crystalline Compound I-l tartaric acid.
• the crystalline Compound I-l tartaric acid has a Compound I-l to tartaric acid ratio of 1 : 1.
• the solid form is characterized by one or more peaks expressed in 2-theta ⁇ 0.2 at about 7.1, 18.3, and 13.2 degrees in an X-Ray powder diffraction pattern obtained using Cu K alpha radiation.
• the solid form is characterized as having an X-ray powder diffraction pattern substantially the same as that shown in Figure lc.
• a specified number range of atoms includes any integer therein.
• a group having from 1-4 atoms could have 1, 2, 3, or 4 atoms.
• compounds of the invention may optionally be substituted with one or more substituents, such as are illustrated generally herein, or as exemplified by particular classes, subclasses, and species of the invention. It will be appreciated that the phrase “optionally substituted” is used interchangeably with the phrase “substituted or unsubstituted.” In general, the term “substituted”, whether preceded by the term “optionally” or not, refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent.
• an optionally substituted group may have a substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position.
• Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds.
• a substituent connected by a bond drawn from the center of a ring means that the substituent can be bonded to any position in the ring.
• J w can be bonded to any position on the pyridyl ring.
• a bond drawn through both rings indicates that the substituent can be bonded from any position of the bicyclic ring.
• J w can be bonded to the 5- membered ring (on the nitrogen atom, for instance), and to the 6-membered ring.
• stable refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, recovery, purification, and use for one or more of the purposes disclosed herein.
• a stable compound or chemically feasible compound is one that is not substantially altered when kept at a temperature of 40°C or less, in the absence of moisture or other chemically reactive conditions, for at least a week.
• aliphatic or "aliphatic group”, as used herein, means a straight-chain (i.e., unbranched), branched, or cyclic, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation that has a single point of attachment to the rest of the molecule.
• aliphatic groups contain 1-20 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-10 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-8 aliphatic carbon atoms. In still other
• aliphatic groups contain 1-6 aliphatic carbon atoms, and in yet other embodiments aliphatic groups contain 1-4 aliphatic carbon atoms.
• Aliphatic groups may be linear or branched, substituted or unsubstituted alkyl, alkenyl, or alkynyl groups. Specific examples include, but are not limited to, methyl, ethyl, isopropyl, n-propyl, sec -butyl, vinyl, n-butenyl, ethynyl, and tert-butyl.
• Aliphatic groups may also be cyclic, or have a combination of linear or branched and cyclic groups.
• Examples of such types of aliphatic groups include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclohexenyl, -CH 2 - cyclopropyl, CH 2 CH 2 CH(CH 3 )-cyclohexyl.
• cycloaliphatic refers to a monocyclic C3-C8 hydrocarbon or bicyclic C 8 -C 12 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point of attachment to the rest of the molecule wherein any individual ring in said bicyclic ring system has 3-7 members.
• cycloaliphatic groups include, but are not limited to, cycloalkyl and cycloalkenyl groups. Specific examples include, but are not limited to, cyclohexyl, cyclopropyl, and cyclobutyl.
• heterocycle means non- aromatic, monocyclic, bicyclic, or tricyclic ring systems in which one or more ring members are an independently selected heteroatom.
• the "heterocycle”, “heterocyclyl”, or “heterocyclic” group has three to fourteen ring members in which one or more ring members is a heteroatom independently selected from oxygen, sulfur, nitrogen, or phosphorus, and each ring in the system contains 3 to 7 ring members.
• heterocycles include, but are not limited to, 3-lH-benzimidazol-2-one, 3-(l-alkyl)-benzimidazol-2-one, 2-tetrahydrofuranyl, 3-tetrahydrofuranyl, 2- tetrahydrothiophenyl, 3-tetrahydrothiophenyl, 2-morpholino, 3-morpholino, 4-morpholino, 2- thiomorpholino, 3-thiomorpholino, 4-thiomorpholino, 1 -pyrrolidinyl, 2-pyrrolidinyl, 3- pyrrolidinyl, 1 -tetrahydropiperazinyl, 2-tetrahydropiperazinyl, 3-tetrahydropiperazinyl, 1- piperidinyl, 2-piperidinyl, 3-piperidinyl, 1-pyrazolinyl, 3-pyrazolinyl, 4-pyrazolinyl, 5- pyrazolinyl, 1 -piperidin
• Cyclic groups (e.g. cycloaliphatic and heterocycles), can be linearly fused, bridged, or spirocyclic.
• heteroatom means one or more of oxygen, sulfur, nitrogen, phosphorus, or silicon (including, any oxidized form of nitrogen, sulfur, phosphorus, or silicon; the quaternized form of any basic nitrogen or; a substitutable nitrogen of a heterocyclic ring, for example N (as in 3,4-dihydro-2H-pyrrolyl), ⁇ (as in pyrrolidinyl) or NR + (as in N- substituted pyrrolidinyl)).
• unsaturated means that a moiety has one or more units of unsaturation.
• unsaturated groups can be partially unsaturated or fully unsaturated. Examples of partially unsaturated groups include, but are not limited to, butene, cyclohexene, and tetrahydropyridine.
• Fully unsaturated groups can be aromatic, anti-aromatic, or non-aromatic. Examples of fully unsaturated groups include, but are not limited to, phenyl, cyclooctatetraene, pyridyl, thienyl, and 1- methylpyridin-2(lH)-one.
• alkoxy or thioalkyl
• haloalkyl mean alkyl, alkenyl or alkoxy, as the case may be, substituted with one or more halogen atoms.
• This term includes perfluorinated alkyl groups, such as -CF 3 and -CF 2 CF 3 .
• halogen means F, CI, Br, or I.
• arylalkoxy refers to monocyclic, bicyclic, and tricyclic ring systems having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic and wherein each ring in the system contains 3 to 7 ring members.
• aryl may be used interchangeably with the term “aryl ring”.
• heteroaryl used alone or as part of a larger moiety as in
• heteroarylalkyl or “heteroarylalkoxy” refers to monocyclic, bicyclic, and tricyclic ring systems having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic, at least one ring in the system contains one or more heteroatoms, and wherein each ring in the system contains 3 to 7 ring members.
• heteroaryl may be used interchangeably with the term “heteroaryl ring” or the term “heteroaromatic”.
• heteroaryl rings include, but are not limited to, 2-furanyl, 3-furanyl, N-imidazolyl, 2- imidazolyl, 4-imidazolyl, 5-imidazolyl, benzimidazolyl, 3-isoxazolyl, 4-isoxazolyl, 5- isoxazolyl, 2-oxazolyl, 4-oxazolyl, 5-oxazolyl, N-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidinyl, 4-pyrimidinyl, 5-pyrimidinyl, pyridazinyl (e.g., 3- pyridazinyl), 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, tetrazolyl (e.g., 5-tetrazolyl), triazolyl (e.g., 2-triazolyl and 5-triazolyl), 2-thien
• heteroaryl includes certain types of heteroaryl rings that exist in equilibrium between two different forms. More specifically, for example, species such hydropyridine and pyridinone (and likewise hydroxypyrimidine and
• pyrimidinone are meant to be encompassed within the definition of "heteroaryl.”
• a protecting group has one or more, or preferably all, of the following characteristics: a) is added selectively to a functional group in good yield to give a protected substrate that is b) stable to reactions occurring at one or more of the other reactive sites; and c) is selectively removable in good yield by reagents that do not attack the regenerated, deprotected functional group.
• the reagents do not attack other reactive groups in the compound. In other cases, the reagents may also react with other reactive groups in the compound.
• nitrogen protecting group refers to an agent used to temporarily block one or more desired nitrogen reactive sites in a multifunctional compound.
• Preferred nitrogen protecting groups also possess the characteristics exemplified for a protecting group above, and certain exemplary nitrogen protecting groups are also detailed in Chapter 7 in Greene, T.W., Wuts, P. G in "Protective Groups in Organic Synthesis", Third Edition, John Wiley & Sons, New York: 1999, the entire contents of which are hereby incorporated by reference.
• a methylene unit of an alkyl or aliphatic chain is optionally replaced with another atom or group.
• R is, for example, H or Ci_ 6 aliphatic.
• R is, for example, H or Ci_ 6 aliphatic.
• R is, for example, H or Ci_ 6 aliphatic.
• R is, for example, H or Ci_ 6 aliphatic.
• R is, for example, H or Ci_ 6 aliphatic.
• R is, for example, H or Ci_ 6 aliphatic.
• R is, for example, H or Ci_ 6 aliphatic.
• methylene unit can also refer to branched or substituted methylene units.
• a nitrogen atom e.g. NR
• dimethylamine e.g. N(CH 3 ) 2 .
• the optional replacements form a chemically stable compound.
• Optional replacements can occur both within the chain and/or at either end of the chain; i.e., both at the point of attachment and/or also at the terminal end.
• Two optional replacements can also be adjacent to each other within a chain so long as it results in a chemically stable compound.
• the optional replacements can also completely replace all of the carbon atoms in a chain.
• a C 3 aliphatic can be optionally replaced by -NR-, -C(O)-, and -NR- to form -NRC(0)NR- (a urea).
• the replacement atom is bound to a hydrogen atom on the terminal end.
• the resulting compound could be -OCH 2 CH 3 , -CH 2 OCH 3 , or -CH 2 CH 2 OH.
• cross-coupling reaction refers to a reaction in which a carbon-carbon bond is formed with the aid of a metal catalyst. Usually, one of the carbon atoms is bonded to a functional group (a "cross-coupling group") while the other carbon atom is bonded to a halogen. Examples of cross coupling reactions include, but are not limited to, Suzuki couplings, Stille couplings, and Negishi couplings.
• cross-coupling group refers to a functional group capable of reacting with another functional group (e.g., halo) in a cross coupling reaction to form a carbon-carbon (“C-C") bond.
• C-C carbon-carbon
• cross coupling condition refers to the chemical conditions (e.g., temperature, length of time of reaction, volume of solvent required) required in order to enable the cross coupling reaction to occur.
• cross-coupling groups and their respective cross-coupling conditions include, but are not limited to, boronic acids and boronic esters with Suzuki coupling conditions, SnBu 3 (Bu: butyl) with Stille coupling conditions, and ZnX (X: halogen) with Negishi coupling conditions.
• All three of these coupling conditions typically involve the use of a catalyst, a suitable solvent, and optionally a base.
• Suzuki coupling conditions involve the use of a palladium catalyst and a suitable solvent.
• suitable palladium catalysts include, but are not limited to, PdCl 2 (PPh 3 ) 2 , Pd(Ph 3 ) 4 , and PdCl 2 (dppf) (wherein each Ph is phenyl, and dppf is l,l-bis(diphenylphosphino)ferrocene).
• Suitable bases include, but are not limited to, K2CO 3 and a 2 C0 3 .
• Suitable solvents include, but are not limited to, tetrahydrofuran, toluene, and ethanol.
• Stille coupling conditions involve the use of a catalyst (usually palladium, but sometimes nickel), a suitable solvent, and other optional reagents.
• a catalyst usually palladium, but sometimes nickel
• suitable solvents include, but are not limited to, tetrahydrofuran, toluene, and dimethylformamide.
• Negishi coupling conditions involve the use of a catalyst (palladium or nickel) and a suitable solvent.
• suitable catalysts include, but are not limited to Pd2(dba)3, Ni(PPh 3 ) 2 Cl 2 , PdCl 2 (PPh 3 ) 2 , and Pd(Ph 3 ) 4 (where "dba" is
• Suitable solvents include, but are not limited to, tetrahydrofuran, toluene, and dimethylformamide.
• cross-coupling groups are formed from coupling group precursors.
• a coupling group precursor is a reagent or group of reagents used to form a cross-coupling group. Examples include, but are not limited to,
• suitable coupling group formation conditions include, but are not limited to, making boronic esters via palladium- mediated catalysis; making boronic acids by hydrolyzing boronic esters; making stannanes via a two step process: 1) halogen metal exchange followed by 2) transmetallation with BusSnCl and making zincates via a two step process: 1) halogen metal exchange followed by 2) addition of ZnC3 ⁇ 4.
• structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, geometric, conformational, and rotational) forms of the structure.
• isomeric e.g., enantiomeric, diastereomeric, geometric, conformational, and rotational
• the R and S configurations for each asymmetric center, (Z) and (E) double bond isomers, and (Z) and (E) conformational isomers are included in this invention.
• a substituent can freely rotate
• any atom not specifically designated as a particular isotope is meant to represent any stable isotope of that atom.
• a position is designated specifically as “H” or “hydrogen”
• the position is understood to have hydrogen at its natural abundance isotopic composition.
• a position is designated specifically as “D” or “deuterium”
• the position is understood to have deuterium at an abundance that is at least 3340 times greater than the natural abundance of deuterium, which is 0.015% (i.e., at least 50.1% incorporation of deuterium).
• structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms.
• compounds having the present structures except for the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a 13 C- or 14 C-enriched carbon are within the scope of this invention.
• Such compounds are useful, for example, as analytical tools or probes in biological assays.
• crystalline refers to a solid that has a specific arrangement and/or conformation of the molecules in the crystal lattice.
• amorphous refers to solid forms that consist of disordered arrangements of molecules and do not possess a distinguishable crystal lattice.
• solvate refers to a crystalline solid adduct containing either stoichiometric or nonstoichiometric amounts of a solvent incorporated within the crystal structure. If the incorporated solvent is water, such adduct is refered to as a "hydrate”.
• Processes and compounds described herein are useful for producing ATR inhibitors that contain an aminopyrazolopyrimidine core.
• the general synthetic procedures shown in schemes herein are useful for generating a wide array of chemical species which can be used in the manufacture of pharmaceutical compounds.
• the anion of commercially available allyl cyanoacetate 1 can react with, e.g., trichloroacetonitrile to provide intermediate 2.
• the anion of commercially available allyl cyanoacetate 1 can be generated with a base such as potassium acetate in an appropriate solvent such as an alcohol (e.g., isopropylalcohol). The anion then reacts with trichloroacetonitrile at room temperature.
• Intermediate 2 then reacts with hydrazine to form the diaminopyrazole 3.
• intermediate 2 is reacted with hydrazine (or its hydrate) in an aprotic solvent, such as DMF, to provide the diaminopyrazole 3.
• aprotic solvent such as DMF
• the reaction occurs under basic conditions (e.g., in the presence of potassium acetate or AcONa) with heating (e.g., ⁇ 1 10°C) to ensure complete cyclisation.
• Intermediate 3 can further be condensed with a dielectrophilic coupling partner to form the pyrimidine 4.
• a dielectrophilic coupling partner e.g., a dielectrophilic coupling partner to form the pyrimidine 4.
• intermediate 3 is reacted with a 1,3- dielectrophilic species (e.g., a 1,3-dialdehyde or a 3-(dialkylamino)-prop-2-enal) in various types of solvents (e.g., DMF or DMSO/water) to furnish the bicyclic cores 4.
• a 1,3- dielectrophilic species e.g., a 1,3-dialdehyde or a 3-(dialkylamino)-prop-2-enal
• solvents e.g., DMF or DMSO/water
• Deprotection, e.g, via hydrolysis, of the allyl ester leads to the carboxylic acids 5.
• compound 4 is subjected to hydro lytic conditions that are known to those skilled in the art. For example, treatment of 4 with phenylsilane or 4- methylbenzenesulfinate in the presence of a catalytic amount of palladium (e.g., Pd(PPh 3 ) 4 ) leads to the formation of the corresponding carboxylic acid 5.
• aqueous alkali e.g., NaOH, LiOH, or KOH
• the carboxylic acids 5 are reacted with amide coupling agents known to those skilled in the art.
• Suitable amide coupling partners include, but are not limited to TBTU, TCTU, HATU, T3P, and COMU.
• the coupling agent is chosen appropriately, the reactions can proceed rapidly ( ⁇ lhr.) at room temperature in the presence of an organic base such as an aliphatic amine (e.g., triethylamine, DIPEA) to provide the activated esters 6a-b.
• an organic base such as an aliphatic amine (e.g., triethylamine, DIPEA)
• activated esters 6a-b prior to the amide bond formation to prepare I-A is generally preferred, although a direct conversion of 5 into the compounds of formula I- A of this invention is also possible.
• Alternative activated esters can also be utilised (isolated or formed in situ) and will be known to those skilled in the art (e.g., using TBTU, TCTU, HATU, T3P, COMU coupling agents).
• activated esters 6a-b can react with substituted 3- aminopyridine 11 to provide compound 1-1 of this invention.
• the reaction conditions for the amide coupling are in a solvent (e.g. anisole, NMP, pyridine, DMF, etc ...) with heating (e.g., > 90°C).
• carboxylic acid 5 can be used as starting points for the amide bond formation, the activated esters being generated in situ, using the same amide couplings agents as those described above.
• Compounds of this invention are isolated in a similar manner to the one described above.
• MS samples were analyzed on a Waters SQD mass spectrometer with electrospray ionization operating in positive and negative ion mode. Samples were introduced into the mass spectrometer using chromatography. All final products had a purity >95%, unless specified otherwise in the experimental details. HPLC purity was measured on a Waters Acquity UPLC system with a Waters SQD MS instrument equipped with a Waters UPLC BEH C8 1.7 ⁇ , 2.1 x 50 mm column and a Vanguard BEH C8 1.7 ⁇ , 2.1 x 5 mm guard column.
• Rt(min) refers to the HPLC retention time, in minutes, associated with the compound. Unless otherwise indicated, the HPLC methods utilized to obtain the reported retention times are as described below:
• the mixture was filtered through a sintered glass funnel to remove the precipitated solid and the filtrate was evaporated under reduced pressure to give a thick liquid.
• DCM approximately 2 L
• the filtrate was purified through a 1 kg silica gel plug (gradient of DCM/MeOH as an eluent), and the solvent was removed to afford an orange solid which was suspended in acetonitrile and heated at about 70°C until all the solid went into solution, at which point the solution was allowed to cool to ambient temperature, then to 2°C.
• the precipitate that formed was isolated by filtration under vacuum, washed with chilled MeCN ( ⁇ 50 mL) and dried to constant mass in a vacuum oven to furnish the title compound as an off-white powder (171.2 g, 41%).
• Step 3 lH-benzo[d] [l,2,3]triazol-l-yl 2-amino-6-fluoropyrazolo[l,5-a]pyrimidine-3- carboxylate 6a
• the organic phase was concentrated in vacuo to a total volume of approx. 6 L, dried (MgS0 4 ), filtered through filter paper and concentrated in vacuo (on a rotary evaporator, 40°C bath temp) until product crystallised out (approx. 2 L of solvent remaining).
• Heptane (2.5 L) was added and the mixture rotated on a rotary evaporator at 40°C.
• the solution was concentrated in vacuo (on a rotary evaporator, 40°C bath temp) to remove more EtOAc until the product crystallised out of solution. The mixture was then left to cool and stand at ambient temperature overnight.
• the solid was collected by filtration through Whatman JVe 1 filter paper, washed with heptane until filtrate ran essentially colourless. The solid was dried for approx. 5 hr. to leave crop 1 of product as an off white solid, 382.51 g.
• Step 2 tert-butyl (5-fluoro-4-iodopyridin-3-yl)carbamate
• reaction mixture was cooled to -28°C (internal temperature), then n-BuLi (1.885 L of 2.5 M in hexanes, 4.712 mol) was added via canula at such a rate as to keep internal temperature below -20°C (i.e., over 2 hr.). On complete addition, the reaction mixture was stirred at between -30 and -20°C (internal temperature) for a further 50 mins. Solid molecular iodine (765.5 g, 3.016 mol) was slowly added in 12 roughly equal portions over 1 hr. (approx. 2/3°C delayed exotherm after each portion added) keeping the internal temperature below -20°C. On complete addition of iodine, the reaction mixture was stirred at -30°C (internal temperature) for a further 45 mins.
• the aqueous phase was removed and the organic phase washed further with a saturated sodium thiosulfate aqueous solution (2 L) and water (1 x 2 L then 1 x 2.5 L) and then brine (2 L).
• the organic phase was concentrated in vacuo (rotary evaporator) to such a volume that the product started to crystallise out to give a thick suspension. The mixture was left to stand at room temperature overnight.
• the mixture was heated under reflux and under a nitrogen atmosphere for 48 hr.
• the mixture was cooled to room temperature then passed through a pad of celite, rinsing through with EtOAc until filtrate almost colourless (approx. 1.5 L).
• the filtrate was concentrated in vacuo to leave a sticky brown solid, 339.7 g.
• Step 4 2-amino-6-fluoro-N-(5-fluoro-4-(l-methyl-lH-imidazol-5-yl)pyridin-3- yl)pyrazolo[l,5-a]pyrimidine-3-carboxamide (Compound I-l)
• the solid was collected by filtration, washed with minimal anisole (approx 20 mL), dried under vacuum for 1 hr., then the solid dried in a vacuum oven at 45°C (internal temperature) for 2 hr. to leave product as a light yellow solid, 7.8 g.
• This solid was suspended in water (78 mL) and MeCN (117 mL) and TFA (2.4 g, 1.62 mL, 1 eq.) was added.
• the reaction mixture was stirred at room temperature for 10 mins. then filtered through filter paper, washed through with small amount of water.
• Solid Forms of Compound I-l has been prepared in various solid forms, including anhydrous forms.
• the solid forms of the present invention are useful in the manufacture of medicaments for the treatment of cancer.
• One embodiment provides use of a solid form described herein for treating cancer.
• the cancer is triple negative breast cancer, pancreatic cancer, small cell lung cancer, colorectal cancer, ovarian cancer, or non-small cell lung cancer.
• Another embodiment provides a pharmaceutical composition comprising a solid form described herein and a pharmaceutically acceptable carrier.
• Compound I-l anhydrous free base can be prepared according to the methods described in Example 1, Step 4.
• thermogravimetric analysis of compound I-l anhydrous free base was performed to determine the percent weight loss as a function of temperature using the Discovery TGA (TA Instruments Trios).
• a sample (2.84mg) was added to a pre-tared aluminum pan and heated from ambient temperature to 400°C at 10°C/min.
• the TGA results seen in Figure 2a show very little observed weight loss prior to melting or thermal degradation. From ambient temperature to 261°C, the weight loss is 0.60%.
• TGA thermal gravimetric analysis
• DSC Differential Scanning Calorimetry of Compound 1-1 (hydrate)
• DSC Differential scanning calorimetry
• a sample (2.78 mg) was weighed in a pinholed aluminum hermetic pan and heated from ambient temperature to 370°C at 10°C/min.
• the DSC results seen in Figure 3b show a broad desolvation endotherm below 100°C followed by a exotherm recrystallization to Compound I-l anhydrous free base between 100- 150°C.
• the endotherm peak between 300-305°C indicates the melting of Compound I-l anhydrous free base.
• TGA thermal gravimetric analysis
• Compound 1-1 tartaric acid form was performed to determine the percent weight loss as a function of temperature using the Discovery TGA (TA Instruments Trios).
• a sample (3.35 mg) was added to a pre-tared aluminum pan and heated from ambient temperature to 330°C at 10°C/min.
• the TGA results seen in Figure 2c show three step weight losses of 12.4%, 12.6%, and 8.5% between 150- 330°C.
• DSC Differential scanning calorimetry
• Compounds can be screened for their ability to inhibit intracellular ATR using an immunofluorescence microscopy assay to detect phosphorylation of the ATR substrate histone H2AX in hydroxyurea treated cells.
• HT29 cells are plated at 14,000 cells per well in 96-well black imaging plates (BD 353219) in McCoy's 5A media (Sigma M8403) supplemented with 10% foetal bovine serum (JRH Biosciences 12003),
• the cells are washed in PBS, fixed for lOmin in 4% formaldehyde diluted in PBS (Polysciences Inc 18814), washed in 0.2% Tween- 20 in PBS (wash buffer), and permeabilised for lOmin in 0.5% Triton X-100 in PBS, all at room temperature.
• the cells are then washed once in wash buffer and blocked for 30min at room temperature in 10% goat serum (Sigma G9023) diluted in wash buffer (block buffer).
• the cells are then incubated for lh at room temperature in primary antibody (mouse monoclonal anti-phosphorylated histone H2AX Serl39 antibody; Upstate 05-636) diluted 1 :250 in block buffer.
• the cells are then washed five times in wash buffer before incubation for lh at room temperature in the dark in a mixture of secondary antibody (goat anti-mouse Alexa Fluor 488 conjugated antibody; Invitrogen A11029) and Hoechst stain (Invitrogen H3570); diluted 1 :500 and 1 :5000, respectively, in wash buffer.
• the cells are then washed five times in wash buffer and finally lOOul PBS is added to each well before imaging.
• Cells are imaged for Alexa Fluor 488 and Hoechst intensity using the BD Pathway 855 Bioimager and Attovision software (BD Biosciences, Version 1.6/855) to quantify phosphorylated H2AX Serl39 and DNA staining, respectively.
• the percentage of phosphorylated H2AX -positive nuclei in a montage of 9 images at 20x magnification is then calculated for each well using BD Image Data Explorer software (BD Biosciences Version 2.2.15).
• Phosphorylated H2AX-positive nuclei are defined as Hoechst-positive regions of interest containing Alexa Fluor 488 intensity at 1.75-fold the average Alexa Fluor 488 intensity in cells not treated with hydroxyurea.
• the percentage of H2AX positive nuclei is finally plotted against concentration for each compound and IC50s for intracellular ATR inhibition are determined using Prism software (GraphPad Prism version 3.0cx for
• Compounds can be screened for their ability to inhibit ATR kinase using a radioactive-phosphate incorporation assay. Assays are carried out in a mixture of 50mM Tris/HCl (pH 7.5), lOmM MgCl 2 and lmM DTT. Final substrate concentrations are 10 ⁇ [ ⁇ -33 ⁇ ] ⁇ (3mCi 33P ATP/mmol ATP, Perkin Elmer) and 800 ⁇ target peptide (ASELPASQPQPFSAKKK). [00137] Assays are carried out at 25°C in the presence of 5 nM full-length ATR.
• An assay stock buffer solution is prepared containing all of the reagents listed above, with the exception of ATP and the test compound of interest. 13.5 ⁇ ., of the stock solution is placed in a 96 well plate followed by addition of 2 ⁇ ⁇ of DMSO stock containing serial dilutions of the test compound (typically starting from a final concentration of 15 ⁇ with 3 -fold serial dilutions) in duplicate (final DMSO concentration 7%). The plate is pre-incubated for 10 minutes at 25°C and the reaction initiated by addition of 15 ⁇ ⁇ [ ⁇ -33 ⁇ ] ⁇ (final concentration 10 ⁇ ).
• the reaction is stopped after 24 hours by the addition of 30 ⁇ , 0.1M phosphoric acid containing 2mM ATP.
• a multiscreen phosphocellulose filter 96-well plate (Millipore, Cat no. MAPHN0B50) is pretreated with ⁇ . 0.2M phosphoric acid prior to the addition of 45 ⁇ ., of the stopped assay mixture.
• the plate is washed with 5 x 200 ⁇ , 0.2M phosphoric acid. After drying, 100 ⁇ ⁇ Optiphase 'SuperMix' liquid scintillation cocktail (Perkin Elmer) is added to the well prior to scintillation counting (1450 Microbeta Liquid Scintillation Counter, Wallac).
• Ki(app) data are calculated from non-linear regression analysis of the initial rate data using the Prism software package (GraphPad Prism version 3.0cx for Macintosh, GraphPad Software, San Diego California, USA).
• the compounds of the present invention are effective for inhibiting ATR.
• Compound 1-1 inhibits ATR at Ki values below 1 ⁇ .
• HCT1 16 cells which possess a defect in ATM signaling to Cisplatin (see, Kim et al; Oncogene 21 :3864 (2002); see also, Takemura et al; JBC 281 :30814 (2006)) are plated at 470 cells per well in 96-well polystyrene plates (Costar 3596) in 150 ⁇ 1 of McCoy's 5A media (Sigma M8403) supplemented with 10% foetal bovine serum (JRH Biosciences 12003),
• Compounds and Cisplatin are then both added simultaneously to the cell media in 2-fold serial dilutions from a top final concentration of ⁇ as a full matrix of concentrations in a final cell volume of 200 ⁇ 1, and the cells are then incubated at 37°C in 5% C0 2 .
• 40 ⁇ 1 of MTS reagent Promega G358a
• absorbance is measured at 490nm using a SpectraMax Plus 384 reader (Molecular Devices) and the concentration of compound required to reduce the IC50 of Cisplatin alone by at least 3 -fold (to 1 decimal place) can be reported.
• the compounds of the present invention are effective for sensitizing cancer cells to Cisplatin.
• Compound 1-1 have Cisplatin sensitization values of ⁇ 0.2 ⁇ .
• HCT1 16 are plated at 470 cells per well in 96-well polystyrene plates (Costar 3596) in 150 ⁇ 1 of McCoy's 5A media (Sigma M8403) supplemented with 10% foetal bovine serum (JRH Biosciences 12003), Penicillin/
• Assays were carried out at 25°C in the presence of 4 nM full-length ATR, 40 nM full-length ATRIP, 40 nM full-length CLK2 and 600 nM TopBP 1(A891 -SI 105).
• An enzyme stock buffer solution was prepared containing all of the reagents listed above, with the exception of target peptide, ATP and the test compound of interest. This enzyme stock was pre-incubated for 30 minutes at 25°C.
• the reaction was stopped after 20 hours by the addition of 30 ⁇ , 0.3 M phosphoric acid containing 2 mM ATP.
• a phosphocellulose filter 96-well plate (Multiscreen HTS MAPHNOB50, Merck-Millipore, Massachusetts, USA) was pretreated with 100 ⁇ . 0.1 M phosphoric acid prior to the addition of 45 ⁇ , of the stopped assay mixture. The plate was washed with 5 x 200 ⁇ , 0.1 M phosphoric acid.
• Ki(app) data were calculated from non-linear regression analysis of the initial rate data using the Prism software package (GraphPad Prism version 6.0c for Macintosh, GraphPad Software Inc., San Diego, USA).

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