EP4676601A1 - Protein kinase inhibitors and uses thereof - Google Patents
Protein kinase inhibitors and uses thereofInfo
- Publication number
- EP4676601A1 EP4676601A1 EP24714122.9A EP24714122A EP4676601A1 EP 4676601 A1 EP4676601 A1 EP 4676601A1 EP 24714122 A EP24714122 A EP 24714122A EP 4676601 A1 EP4676601 A1 EP 4676601A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- compound
- family
- abl1
- cancer
- substituted
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Pending
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D239/00—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings
- C07D239/70—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings condensed with carbocyclic rings or ring systems
- C07D239/72—Quinazolines; Hydrogenated quinazolines
- C07D239/78—Quinazolines; Hydrogenated quinazolines with hetero atoms directly attached in position 2
- C07D239/84—Nitrogen atoms
-
- 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
- C07D—HETEROCYCLIC COMPOUNDS
- C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
- C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
- C07D403/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings directly linked by a ring-member-to-ring-member bond
Definitions
- PKs typically is referred to by the three or four letter code afforded to the gene that encodes the PK protein.
- PKs are categorized into PK families according to polypeptide sequence and/or function. Dysregulation of PK genes and their encoded PKs are associated with certain cancers.
- the ABL1 protooncogene for example, which also is known as ABL, JTK7, p150, c-ABL, CHDSKM, c-ABL1, encodes an ABL1 PK implicated in processes of cell differentiation, cell division, cell adhesion, and stress response. Activity of the ABL1 PK is negatively regulated by its SH3 polypeptide domain.
- Modification to the ABL1 protooncogene such as deletion of the SH3 domain-encoding portion and fusion with another protein, for example, can turn it into an oncogene.
- Translocation and head-to-tail fusion of the BCR and ABL1 genes is present in cases of chronic myeloid leukemia (CML) and in a subset of acute lymphoblastic leukemia (i.e., Philadelphia chromosome-positive ALL).
- CML chronic myeloid leukemia
- ALL Philadelphia chromosome-positive ALL
- PKs include ABL, BTK, AURK, JAK, TRK, RET, EPH, TNK, PLK, IRAK and TYK family PKs, and may be used for treating cancers and other medical conditions.
- Compounds herein contain a quinazolinyl group, an amine-linked phenyl group and substituents that can afford PK inhibitory activity.
- Compounds herein can inhibit multiple PKs in certain embodiments.
- Compounds herein can selectively inhibit at least one PK in certain instances.
- Compounds that inhibit one or more particular protein kinases (PKs) can be used to treat cancers and other medical conditions.
- FIG.1 illustrates processes of a fluorescence-based PTK substrate peptide assay.
- FIG.2 illustrates amino acid substitutions identified in certain ABL1 variants.
- FIG.3 to FIG.10C show PK inhibition by compounds determined by peptide cleavage and tracer displacement assays.
- FIG.3 shows inhibition of ABL family PKs.
- FIG.4 shows inhibition of BTK family PKs.
- FIG.5 shows inhibition of AURK family PKs.
- FIG.6 shows inhibition of JAK family PKs.
- FIG.7 shows inhibition of TRK family PKs.
- FIG.8 shows inhibition of RET family PKs.
- FIG.9A shows inhibition of EPH family PKs.
- FIG. 9B shows inhibition of TNK family, PLK family and IRAK family PKs.
- FIG.9C shows inhibition of SRC and DDR family PKs.
- FIG.9D shows inhibition of ABL2 and PTK2B PKs.
- FIG.10A shows inhibition of ABL and BTK family PKs.
- FIG.10B shows inhibition of ABL and AURK family PKs.
- FIG. 10C shows inhibition of ABL, BTK and AURK family PKs.
- the legend at the bottom of FIG.3 is applicable to charts in FIG.4 to FIG.10C.
- PK inhibitor drugs can present issues including ineffectiveness in a patient subgroup, loss of therapeutic effect during treatment for a patient subgroup, and triggering a serious adverse event in a patient subgroup.
- an amino acid substitution in the ABL1 kinase domain occurring in a patient can impart resistance to cancer treatment.
- An ABL1 variant containing a threonine 315 to isoleucine (T315I) amino acid substitution can result in resistance to cancer treatment, for example.
- Certain compounds herein can effectively inhibit the ABL1(T315I) variant. Certain compounds herein can effectively inhibit other PKs, can effectively inhibit multiple PKs in different PK families and/or can selectively inhibit a PK.
- R 2 R1 R3 Formula A where: R 1 , R 2 and R 3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R 4 , R 5 and R 6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo.
- R 1 , R 2 and R 3 each independently is hydrogen, methyl or methoxy.
- R 4 , R 5 and R 6 each independently is hydrogen, fluoro, chloro, isopropyl, or isopropyloxy.
- R 1 , R 2 and R 3 is methyl or methoxy and the other two of R 1 , R 2 and R 3 each is hydrogen. In certain instances, R 1 is methyl or methoxy and R 2 and R 3 each is hydrogen. In certain embodiments, R 1 is methyl and R 2 and R 3 each is hydrogen. In certain instances, R 3 is methyl or methoxy and R 1 and R 2 each is hydrogen. In certain embodiments, R 3 is methyl and R 1 and R 2 each is hydrogen. In certain instances, R 1 , R 2 and R 3 each is hydrogen, and sometimes R 5 is hydrogen. In certain embodiments, R 4 , R 5 and R 6 each is hydrogen.
- R 2 Formula B or a pharmaceutically acceptable salt thereof, where: R 1 , R 2 and R 3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R 7 , R 8 and R 9 each independently is hydrogen or optionally substituted C1-C6 alkyl.
- R 1 , R 2 and R 3 each independently is hydrogen, methyl or methoxy.
- R 7 , R 8 and R 9 each independently is hydrogen or isobutyl.
- one of R 1 , R 2 and R 3 is methyl or methoxy and the other two of R 1 , R 2 and R 3 are hydrogen.
- R 1 , R 2 and R 3 each is hydrogen, and sometimes R 8 and R 9 each is hydrogen.
- m is the integer of 1, the nitrogen bound to the R 47 has a covalently bound hydrogen, as depicted in Formula D.
- m is the integer 1 and the compound is of Formula D: R 2 R 1 R 3 N Formula D each independently is hydrogen, methyl or methoxy.
- one of R 1 , R 2 and R 3 is methyl or methoxy and the other two of R 1 , R 2 and R 3 are hydrogen.
- R 1 , R 2 and R 3 each is hydrogen.
- R 10 , R 11 , R 12 and R 13 each independently is hydrogen or methoxy.
- R 10 and R 12 each is hydrogen, and sometimes R 11 and R 13 each is methoxy.
- n is an integer of 3 to 7.
- a Subgroup 1 compound is of Formula A, where R 1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R 2 , R 3 and R 5 each is hydrogen; and R 4 and R 6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo, with the proviso that R 4 or R 6 , or R 4 and R 6 , is not hydrogen.
- R 1 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
- R 4 is unsubstituted C1-C4 alkoxy or isopropyloxy;
- R 6 is fluoro or chloro; or a combination of (i) and (ii).
- a Subgroup 1 compound is 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2- yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C1); 4-((5-((8-(4-fluoro-2- isopropoxyphenyl)quinazolin-2-yl)amino)-2-methoxyphenyl)carbamoyl)benzoic acid (compound C3); 4-((5-((8-(2-isopropylphenyl)quinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C4); or a pharmaceutically acceptable salt thereof.
- a Subgroup 2 compound is of Formula A, where R 1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R 2 , R 3 , R 4 , R 5 and R 6 each is hydrogen.
- R 1 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
- a Subgroup 2 compound is 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid (compound C12) or a pharmaceutically acceptable salt thereof.
- a Subgroup 3 compound is of Formula A, where R 3 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R 1 , R 2 , R 4 , R 5 and R 6 each is hydrogen.
- R 3 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
- a Subgroup 3 compound is 4-((4-methyl-3-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid (compound C13) or a pharmaceutically acceptable salt thereof.
- a compound is of Formula C or Formula D with the proviso that R 12 is not methoxy.
- a composition contains a compound of Formula C or Formula D with the proviso that R 12 is not O N O O S .
- a compound of Formula C or Formula D with the proviso that R 11 or R 13 is not O .
- a composition contains a compound according to Formula A, Formula B, Formula C or Formula D with the proviso that R 1 and R 2 , or optionally R 2 and R 3 , do not join to form an imidazolyl group.
- a composition contains a compound according to Formula A, Formula B, Formula C or Formula D with the proviso that R 1 and R 2 , or optionally R 2 and R 3 , are not joined as: (i) an imidazolyl moiety fused to the phenyl group on which R 2 , R 3 and R 4 are substituents; (ii) an indolyl group; (iii) a five-membered ring; (iv) a five-membered ring fused to the phenyl group on which R 1 , R 2 and R 3 are substituents; (v) unsubstituted heteroaryl containing 5 ring atoms; and/or (vi) substituted heteroaryl containing 5 ring atoms.
- a composition contains a compound according to Formula A, Formula B, Formula C or Formula D with the proviso that R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R 11 , R 12 , R 13 , R 14 or R 15 each independently is not: (i) one of the following designated Group A electrophilic groups: ; (ii) one of the following designated Group B electrophilic groups: ; and/or (iii) an electrophilic group capable of forming a covalent bond with a cysteine of a protein.
- a compound herein is provided as a hydrochloride salt.
- a composition contains a compound, or a combination of two or more of the compounds, described in the following Table A (the term "Compound” is abbreviated by "Cmpd” in the header row of Table A).
- Table A Cmpd Structure Name (IUPAC) d d id Cmpd Structure Name (IUPAC) - n- - id id Cmpd Structure Name (IUPAC)
- IUPAC Cmpd Structure Name
- a composition described herein is provided as a pharmaceutical composition.
- a compound in a composition described herein binds to an ABL1 polypeptide.
- a compound in a composition described herein inhibits an activity of an ABL1 polypeptide.
- a compound binds to two or more ABL1 variant polypeptides. In certain instances, a compound inhibits an activity of two or more ABL1 variant polypeptides. In certain implementations, a compound is an effective inhibitor of two or more ABL1 variant polypeptides. In certain implementations, a composition described herein is for inhibition of an activity of an ABL1 polypeptide or ABL1 variant polypeptide. In certain instances, a composition described herein is for inhibition of a catalytic activity of an ABL1 polypeptide or ABL1 variant polypeptide. In certain instances, a composition described herein is for treatment of a condition, which sometimes is an ABL1-related condition.
- the condition is a cancer, and sometimes the cancer is a leukemia.
- the leukemia is chronic myeloid leukemia or acute lymphoblastic leukemia.
- a number or letter normally designated as a superscript for example, the “1” in R 1 , or the “L” in R L
- a subscript for example, R 1 or R L
- Any definition herein may be used in combination with any other definition to describe a composite structural group.
- substituted refers, without limitation, to one or more substituents that can include, for example, substituents independently selected from the following groups or a particular designated set of groups, alone or in combination: lower alkyl, lower alkenyl, lower alkynyl, lower alkanoyl, lower heteroalkyl, lower aryl, lower cycloalkyl, lower heteroaryl, lower heterocycloalkyl, aryl, cycloalkyl, heteroaryl, heterocycloalkyl, lower haloalkyl, lower haloalkenyl, lower haloalkynyl, lower perhaloalkyl, lower perhaloalkoxy, phenyl, aryloxy, lower hydroxyalkyl, lower mercaptoalkyl, lower aminoalkyl, lower arylaminoalkyl, aryloxyalkyl, lower aryloxyalkyl, arylthioalkyl, lower arylthioalkyl, lower arylthioalkyl
- Two substituents may be joined together to form a fused five-, six-, or seven-membered carbocyclic, heterocyclic aryl, or heteroaryl ring system having zero to three heteroatoms, for example, forming methylenedioxy or ethylenedioxy.
- An optionally substituted group may contain a deuterium in place of one or more hydrogen atoms (e.g., -CD3 instead of -CH3).
- An optionally substituted group may be unsubstituted (e.g., -CH2CH3), fully substituted (e.g., -CF2CF3), monosubstituted (e.g., - CH2CH2F) or substituted at a level anywhere in-between fully substituted and monosubstituted (e.g., -CH2CF3).
- substituents are recited without qualification as to substitution, both substituted and unsubstituted forms are encompassed.
- substituent is qualified as “substituted,” the substituted form is specifically intended.
- different sets of optional substituents to a particular moiety may be defined as needed.
- R or the term R’ appearing by itself and without a number designation, unless otherwise defined, refers to a moiety chosen from hydrogen (H), alkyl, cycloalkyl, heteroalkyl, aryl, heteroaryl and heterocycloalkyl, any of which may be optionally substituted.
- any variable, substituent, or term e.g. aryl, heterocycle, R, etc.
- its definition at each occurrence is independent of the definition at every other occurrence.
- Certain groups may be attached to a parent molecule or may occupy a position in a chain of elements from either end as written.
- an asymmetrical group such as –C(O)N(R)– may be attached to a parent moiety at either the carbon or the nitrogen.
- the term ‘substituted’ and ‘substituent group’ means a group selected from the following moieties: (A) oxo, halogen, -CCl 3 , -CBr 3 , -CF 3 , -CI 3 , -CHCl 2 , -CHBr 2 , -CHF 2 , -CHI 2 , -CH 2 Cl, -CH 2 Br, -CH 2 F, -CH 2 I, -OCCl 3 , -OCF 3 , -OCBr 3 , -OCI 3 , -OCHCl 2 , -OCHBr 2 , -OCHI 2 , -OCHF 2 , -OCH 2 Cl, -OCH 2 Br, -OCH 2 I, -OCH 2 F, -CN, -OH, -NH 2 , -COOH, -CONH 2 , -NO2, -SH,
- a “size-limited substituent” or “size-limited substituent group,” as used herein, means a group selected from all of the substituents described above for a “substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C 1 -C 20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -C 10 aryl, and each substituted or unsubstituted heteroaryl is
- each substituted group described in the compounds herein is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In some embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group. In some embodiments, at least one or all of these groups are substituted with at least one lower substituent group.
- each substituted or unsubstituted alkyl may be a substituted or unsubstituted C 1 -C 20 alkyl
- each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl
- each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 8 cycloalkyl
- each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl
- each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -C 10 aryl
- each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl.
- each substituted or unsubstituted alkylene is a substituted or unsubstituted C 1 -C 20 alkylene
- each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered heteroalkylene
- each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C8 cycloalkylene
- each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene
- each substituted or unsubstituted arylene is a substituted or unsubstituted C6- C10 arylene
- each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered heteroarylene.
- each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C8 alkylene
- each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene
- each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C7 cycloalkylene
- each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene
- each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene
- each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene.
- the compound is a chemical species set forth in the Examples section, figures, or tables below.
- a substituted or unsubstituted moiety e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is unsubstituted (e.g., is an unsubstituted alkyl, unsubstituted heteroalkyl, substituted or un
- a substituted or unsubstituted moiety e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is substituted (e.g., is a substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alky
- a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
- is substituted with at least one substituent group wherein if the substituted moiety is substituted with a plurality of substituent groups, each substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of substituent groups, each substituent group is different.
- a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
- is substituted with at least one size-limited substituent group wherein if the substituted moiety is substituted with a plurality of size-limited substituent groups, each size-limited substituent group may optionally be different.
- each size-limited substituent group is different.
- a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
- each lower substituent group is different.
- a substituted moiety e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene
- alkoxy refers to an alkyl ether radical, where the term alkyl is as defined below.
- alkyl ether radicals include methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, and the like.
- alkyl refers to a saturated straight-chain or branched-chain hydrocarbon radical containing from 1 to 20 carbon atoms.
- the term “straight-chain alkyl” refers to a saturated straight-chain hydrocarbon radical.
- the term “branched-chain alkyl” refers to a saturated branched-chain hydrocarbon radical.
- an alkyl includes 1 to 10 carbon atoms (C1-C10 alkyl), 1 to 8 carbon atoms (C1-C8 alkyl), 1 to 6 carbon atoms (C1-C6 alkyl) or 1 to 3 carbon atoms (C1-C3 alkyl).
- Alkyl groups may be optionally substituted as defined herein.
- alkyl radicals include methyl, ethyl, n- propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl, nonyl and the like.
- alkylene refers to a saturated aliphatic group derived from a straight or branched chain saturated hydrocarbon attached at two or more positions, such as methylene (–CH 2 –). Unless otherwise specified, the term “alkyl” may include “alkylene” groups.
- alkylamino refers to an alkyl group attached to a parent molecular moiety through an amino group.
- Alkylamino groups include monoalkylated groups (monoalkylamino) or dialkylated groups (dialkylamino), non-limiting examples of which include N-methylamino, N-ethylamino, N,N-dimethylamino, N,N-ethylmethylamino and the like.
- dialkylamino dialkylated groups
- C-amido refers to a -C(O)N(RR’) group with R and R’ as defined herein or as defined by the specifically enumerated “R” groups designated.
- N-amido refers to a RC(O)N(R’)- group, with R and R’ as defined herein or as defined by the specifically enumerated “R” groups designated.
- acylamino as used herein, alone or in combination, includes an acyl group attached to a parent moiety through an amino group.
- a non-limiting example of an "acylamino” group is acetylamino (CH3C(O)NH–).
- amino refers to -NRR’, where R and R’ are independently chosen from hydrogen, alkyl, alkenyl, alkynyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R’ may combine to form heterocycloalkyl or heteroaryl, either of which may be optionally substituted.
- aminoalkyl refers to an amino group attached to a parent molecule through an alkyl group (N(R)(R')-alkyl-), where R and R' are defined herein.
- lower aminoalkyl refers to an amino group attached to a parent molecule through a lower alkyl group (N(R)(R')-lower alkyl-), where “lower alkyl,” R and R' are defined herein.
- aryl refers to an aromatic cyclic ring system, or aromatic hydrocarbon ring system, in which all of the atoms that form the covalent structure of the one or more aromatic rings are carbon (referred to herein as an “aryl ring”).
- the aryl ring may be optionally substituted as defined herein.
- the ring system may be monocyclic or fused polycyclic, for example, bicyclic or tricylic (containing two or three rings fused together).
- the monocyclic aryl ring is C4-C10, or C5-C9, or C5-C8, or C5-C7, or, in certain embodiments, C5- C6, where these carbon numbers refer to the number of carbon ring member atoms that form the ring system.
- the polycyclic ring system is a bicyclic aryl group, where the bicyclic aryl group in some embodiments is C8-C12, or, for example, C9-C10.
- the polycyclic ring system is a tricyclic aryl group, where the tricyclic aryl group is C11-C18, or, for example, C12-C16.
- aryl ring systems include phenyl (monocyclic, C6), naphthyl (bicyclic, C10), anthracenyl (tricyclic, C14) and phenanthryl (tricyclic, C14).
- arylalkyl or “aralkyl,” as used herein, alone or in combination, refers to an aryl group attached to a parent molecular moiety through an alkyl group.
- lower arylalkyl or “lower aralkyl,” as used herein, alone or in combination, refers to a lower aryl group attached to a parent molecular moiety through a lower alkyl group, where "lower aryl” and “lower alkyl” are as defined herein.
- arylalkynyl or “aralkynyl,” as used herein, alone or in combination, refers to an aryl group attached to a parent molecular moiety through an alkynyl group.
- arylaminoalkyl refers to an aryl group attached to a parent molecule through an aminoalkyl group (aryl-N(R)-alkyl-), where R is as defined herein.
- lower arylaminoalkyl refers to a lower aryl group attached to a parent molecule through a lower aminoalkyl group (lower aryl-N(R)-lower alkyl-), where "lower aryl,” “lower aminoalkyl” and R are as defined herein.
- benzo and “benz,” as used herein, alone or in combination, refer to the divalent radical C6H4 derived from benzene.
- Non-limiting examples include benzothiophene and benzimidazole.
- carbamate refers to an ester of carbamic acid (—NHCOO–) which may be attached to a parent molecular moiety from either the nitrogen or acid end, and which may be optionally substituted as defined herein.
- O-carbamyl refers to a -OC(O)NRR’ group where R and R’ are as defined herein.
- N-carbamyl as used herein, alone or in combination, refers to a ROC(O)NR’- group, where R and R’ are defined herein.
- carbonyl when alone includes formyl [–C(O)H] and in combination includes a –C(O)– group.
- carboxyl or “carboxy,” as used herein, refers to –C(O)OH or the corresponding “carboxylate” anion (e.g., in a carboxylic acid salt).
- An “O-carboxy” group refers to a RC(O)O– group, where R is as defined herein.
- a “C-carboxy” group refers to a –C(O)OR group where R is as defined herein.
- cycloalkyl and, interchangeably, “carbocycle,” as used herein, alone or in combination, refers to a ring system in which all of the ring member atoms are carbon and at least one of the rings is a saturated or partially unsaturated aliphatic cyclic ring moiety (referred to herein as a “cycloalkyl ring” or “carbocycle ring”).
- each cyclic moiety contains from 3 to 12 carbon ring member atoms which may be optionally substituted as defined herein.
- a cycloalkyl group contains 3 to 10 carbon ring member atoms.
- a cycloalkyl includes 5 to 7 carbon atoms.
- a cycloalkyl includes 5 to 6 carbon atoms.
- a cycloalkyl can be a monocyclic or polycyclic, e.g., bicyclic or tricyclic, ring system in which at least one cyclic ring is a cycloalkyl ring.
- the monocyclic cycloalkyl ring is C3-C10, or C5-C9, or C5-C8, or C5-C7, or, in certain embodiments, C5-C6, where these carbon numbers refer to the number of carbon ring member atoms that form the ring system.
- Polycyclic cycloalkyl ring systems include fused, bridged and spiro-fused rings.
- Polycyclic cycloalkyl ring systems as defined herein include ring systems in which one or more cycloalkyl rings is/are fused to one or more aryl rings (benzo-fused cycloalkyl ring systems) and/or other cycloalkyl rings. In some embodiments, all of the rings in a polycyclic cycloalkyl ring system are cycloalkyl rings. In some embodiments, the polycyclic ring system is a bicyclic cycloalkyl group, where the bicyclic cycloalkyl group in some embodiments is C8-C12, or, for example, C9-C10.
- the polycyclic ring system is a tricyclic cycloalkyl group, where the tricyclic cycloalkyl group is C11-C18, or, for example, C12-C16.
- cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, octahydronaphthalene, decahydronaphthalene, bicyclo[1,1,1]pentane and the like.
- aryl-fused cyclolalkyl ring systems include a benzene ring fused to hydrogenated or partially hydrogenated ring systems, non-limiting examples of which include dihydronaphthalene, tetrahydronaphthalene and indanyl.
- attachment of the polycycle to the indicated point of attachment on the parent molecule may be through any ring atom of the polycycle rings.
- the polycycle is attached to the indicated point of attachment through a ring member atom of a cycloalkyl ring.
- the polycycle is attached to the indicated point of attachment through a ring member atom of a ring that is not a cycloalkyl ring, e.g., an aryl ring.
- ether refers to an oxy group bridging two moieties linked at carbon atoms.
- halo refers to fluorine, chlorine, bromine, or iodine.
- haloalkoxy refers to a haloalkyl group attached to a parent molecular moiety through an oxygen atom.
- haloalkyl refers to an alkyl radical having the meaning as defined above where one or more hydrogens are replaced with a halogen.
- a monohaloalkyl radical for example, sometimes include an iodo, bromo, chloro or fluoro atom within the radical.
- Dihalo and polyhaloalkyl radicals sometimes include two or more of the same halo atoms or a combination of different halo radicals.
- Non-limiting examples of haloalkyl radicals include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl.
- Haloalkylene refers to a haloalkyl group attached at two or more positions. Non-limiting examples include fluoromethylene (—CFH—), difluoromethylene (–CF2 –), chloromethylene (–CHCl–) and the like.
- heteroaliphatic refers to an aliphatic moiety, as defined herein, that contains one or more heteroatoms, such as, for example, oxygen, nitrogen, sulfur, phosphorous and/or silicon, e.g., in place of a carbon atom or between carbon atoms.
- a heteroaliphatic group contains from one to three heteroatoms chosen from O, N, and S, and where the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized.
- the heteroatom(s) may be placed at any interior position of the heteroaliphatic group. In some embodiments, up to two heteroatoms may be consecutive.
- a heteroaliphatic group includes 2 to 20 carbon atoms, 2 to 10 carbon atoms, 2 to 8 carbon atoms or 2 to 6 carbon atoms.
- heteroalkyl refers to a saturated or unsaturated, stable straight or branched hydrocarbon chain having the stated number of carbon atoms and one or more heteroatoms, such as, for example, oxygen, nitrogen, sulfur, phosphorous and/or silicon, e.g., in place of a carbon atom.
- a heteroalkyl contains from one to three heteroatoms chosen from O, N, and S, and where the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized.
- the heteroatom(s) may be placed at any interior position of the heteroalkyl group. In some embodiments, up to two heteroatoms may be consecutive, such as, for example, -CH 2 -NH- OCH 3 .
- a heteroalkyl includes 2 to 20 carbon atoms, 2 to 10 carbon atoms, 2 to 8 carbon atoms or 2 to 6 carbon atoms. In some instances, a heteroalkyl contains from 1 to 3 degrees of unsaturation.
- Heteroalkyl groups may be optionally substituted as defined herein.
- the heteroaryl ring may be optionally substituted as defined herein.
- a heteroaryl can be a monocyclic or a fused polycyclic, e.g., bicyclic or tricyclic, ring system in which at least one cyclic ring is an aromatic heteroaryl ring.
- Polycyclic, e.g., bicyclic and tricyclic, fused heteroaryl ring systems as defined herein include heteroaryl ring systems in which one or more heteroaryl rings is/are fused to one or more aryl rings (which are referred to herein as aryl-fused heteroaryl rings), one or more cycloalkyl rings and/or one or more other heteroaryl rings. In some embodiments, all of the rings in a polycyclic heteroaryl ring system are heteroaryl rings. In certain embodiments, a heteroaryl ring contains at least one atom chosen from O, S, and N. In certain embodiments, a heteroaryl ring is a 3 to 15 membered monocyclic ring.
- a monocyclic heteroaryl group may contain from 4 to 10 ring member atoms, and may have, for example, 1 to 4 heteroatoms in the ring, where the remaining ring member atoms are carbon.
- a bicyclic heteroaryl ring may contain from 8 to 15 ring member atoms, and have from 1 to 8 heteroatoms, where the remaining ring member atoms are carbon.
- a tricyclic heteroaryl ring may contain from 11 to 18 ring member atoms, and have from 1 to 10 heteroatoms, where the remaining ring member atoms are carbon.
- heteroaryls include pyrrolyl, pyrrolinyl, imidazolyl, pyrazolyl, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, tetrazinyl, triazolyl, tetrazolyl, furyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, thiadiazolyl, isothiazolyl, indolyl, isoindolyl, indolizinyl, benzimidazolyl, quinolyl, isoquinolyl, quinoxalinyl, quinazolinyl, indazolyl, benzotriazolyl, thienopyridinyl, furopyridinyl, pyrrolopyridinyl and the like.
- Exemplary bicyclic and tricyclic heteroaryl groups include phenanthrolinyl, dibenzofuranyl, acridinyl, phenanthridinyl, dihydro[1,3]oxazolo[4,5-b]pyridinyl, benzothiazolyl, and the like.
- attachment of the polycycle to the indicated point of attachment on the parent molecule may be through any ring member atom of the polycycle rings.
- the polycycle is attached to the indicated point of attachment through a ring member atom of a heteroaryl ring.
- the monocyle or polycycle is attached to the indicated point of attachment through a ring member heteroatom of a heteroaryl ring.
- the polycycle is attached to the indicated point of attachment through a ring member atom of a ring that is not a heteroaryl ring, e.g., an aryl ring or a cycloalkyl ring.
- Heteroaryl includes sulfones, sulfoxides, N-oxides of tertiary nitrogen ring member atoms, and carbocyclic fused and benzo-fused ring systems.
- heteroaryl group may be referred to as an aryl group having one or more carbon atoms substituted with O, NR n , S, SO, SO 2 , where “n” denotes any positive integer.
- heteroarylalkyl refers to an unsubstituted or substituted heteroaryl group attached to a parent molecular moiety through an alkyl group.
- lower heteroarylalkyl refers to an unsubstituted or substituted lower heteroaryl group attached to a parent molecular moiety through a lower alkyl group where "lower heteroaryl” and “lower alkyl” are as defined herein.
- heteroarylaminoalkyl refers to a heteroaryl group attached to a parent molecule through an aminoalkyl group (heteroaryl-N(R)-alkyl-), where R is as defined herein.
- lower heteroarylaminoalkyl refers to a lower heteroaryl group attached to a parent molecule through a lower aminoalkyl group (lower heteroaryl-N(R)-lower alkyl-), where "lower heteroaryl,” “lower alkyl” and R are as defined herein.
- heterocycle-alkyl refers to a substituted or unsubstituted heterocycle group attached to a parent molecular moiety through an alkyl group.
- heterocycloalkyl and, interchangeably, “heterocycle,” or “heterocyclic” as used herein, alone or in combination, each refer to a ring system in which at least one of the rings is a saturated or partially unsaturated, heteroaliphatic, nonaromatic cyclic ring moiety in which all of the ring member atoms are carbon, except for at least one heteroatom (referred to herein as a “heterocycloalkyl ring,” “heterocycle ring” or “heterocyclic ring”).
- the one or more heteroatoms that can be in the ring include, for example, nitrogen, oxygen, sulfur, phosphorous and/or silicon.
- the ring heteroatom or heteroatoms is selected from nitrogen, oxygen and sulfur.
- the heterocycloalkyl ring may be optionally substituted as defined herein.
- a heterocycloalkyl is a monocyclic or polycyclic, e.g., bicyclic or tricyclic, ring system in which at least one cyclic ring is a heterocycloalkyl ring.
- Polycyclic heterocycloalkyl ring systems include fused, bridged and spiro- fused rings.
- Polycyclic heterocycloalkyl ring systems as defined herein include ring systems in which one or more heterocycloalkyl rings is/are fused to one or more cycloalkyl, aryl, heteroaryl and/or heterocycloalkyl rings. In some embodiments, all of the rings in a polycyclic heterocycloalkyl ring system are heterocycloalkyl rings. In certain embodiments, a heterocycloalkyl includes 1 to 4 heteroatoms as ring member atoms. In some embodiments, a heterocycloalkyl moiety includes 1 to 2 heteroatoms as ring member atoms. In certain embodiments, a heterocycloalkyl moiety includes 3 to 8 ring member atoms in each ring.
- a heterocycloalkyl moiety includes 3 to 7 ring member atoms in each ring. In yet some embodiments, a heterocycloalkyl moiety includes 5 to 6 ring member atoms in each ring. In some embodiments, a heterocycloalkyl can be a 3 to 15 membered nonaromatic ring, or a fused bicyclic, or tricyclic non-aromatic ring, which contains at least one atom chosen from O, S, and N. In certain embodiments, a monocyclic heterocycloalkyl or heterocycle group may contain from 4 to 10 ring member atoms, and may have, for example, 1 to 4 heteroatoms in the ring, where the remaining ring member atoms are carbon.
- a bicyclic heterocycloalkyl or heterocycle group may contain from 8 to 15 ring member atoms, and have from 1 to 8 heteroatoms, where the remaining ring member atoms are carbon.
- a tricyclic heterocycloalkyl or heterocycle group may contain from 11 to 18 ring member atoms, and have from 1 to 10 heteroatoms, where the remaining ring member atoms are carbon.
- the term also includes fused polycyclic groups where one or more heterocyclic rings are fused with one or more cycloalkyl rings, aryl, heteroaryl and/or other heterocyclic groups.
- attachment of the polycycle to the indicated point of attachment on the parent molecule may be through any ring member atom of the polycycle rings.
- the polycycle is attached to the indicated point of attachment through a ring member atom of a heterocycloalkyl ring.
- the monocyle or polycycle is attached to the indicated point of attachment through a ring member heteroatom of a heterocycloalkyl ring.
- the polycycle is attached to the indicated point of attachment through a ring member atom of a ring that is not a heterocycloalkyl ring, e.g., an aryl ring, heteroaryl ring or a cycloalkyl ring.
- heterocycloalkyl and heterocycle include sulfones, sulfoxides and N-oxides of tertiary nitrogen ring member atoms.
- heterocycle groups include aziridinyl, azetidinyl, 1,3-dioxanyl, 1,4-dioxanyl, 1,3-dioxolanyl, morpholinyl, piperazinyl, pyrrolidinyl, piperidinyl, thiomorpholinyl, pyranyl, dihydropyridinyl, tetrahydropyridinyl, carabazolyl, xanthenyl, 1,3-benzodioxolyl, dihydroisoquinolinyl, dihydrocinnolinyl, dihydrobenzodioxinyl, isoindolinyl, dihydroisoindolyl and dihydroindolyl, and the like.
- heterocycle groups may be optionally substituted unless specifically prohibited.
- Non- limiting examples of heterocycloalkyl groups may be referred to as cycloalkyl group having one or more carbon atoms substituted with O, NR n , S, SO, SO2, where n denotes any positive integer.
- hydroxy as used herein, alone or in combination, refers to –OH.
- the phrase “in the main chain” refers to the longest contiguous or adjacent chain of carbon atoms starting at the point of attachment of a group to the compounds of any one of the formulas disclosed herein.
- linear chain of atoms refers to the longest straight chain of atoms independently selected from carbon, nitrogen, oxygen and sulfur.
- lower means a moiety containing from 1 to and including 6 carbon atoms.
- lower aryl means a C4-C6 aryl group, for example, a C5-C6 aryl group.
- a lower aryl group sometimes is a C4-C6 aryl ring group, or C5-C6 aryl ring group for example, including without limitation, phenyl.
- the term may also refer to a C8- C10 bicyclic ring aryl group, for example, including without limitation, napthyl.
- Lower aryl groups, including phenyl or napthyl may be optionally substituted as provided.
- lower heteroaryl means a four-membered, five-membered, or six-membered heteroaryl group.
- a lower heteroaryl group sometimes is (1) a monocyclic heteroaryl ring comprising five or six ring member atoms, of which between one and four of the ring member atoms may be heteroatoms chosen from O, S, and N, or (2) a bicyclic heteroaryl ring, where each of the fused rings comprises five or six ring member atoms, comprising between them one to four heteroatoms chosen from O, S, and N.
- Lower heteroaryl groups may be optionally substituted as provided.
- lower cycloalkyl means a monocyclic cycloalkyl having between three and six ring member atoms.
- Non-limiting examples of lower cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
- Lower cycloalkyl groups may be optionally substituted as provided.
- lower heterocycloalkyl as used herein, alone or in combination, means a monocyclic heterocycloalkyl having between three and six ring member atoms, of which between one and four may be heteroatoms chosen from O, S, and N.
- Non-limiting examples of lower heterocycloalkyls include pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, and morpholinyl.
- Lower heterocycloalkyl groups may be optionally substituted as provided.
- the term “lower amino,” as used herein, alone or in combination, refers to -NRR’, where R and R’ are independently chosen from hydrogen, lower alkyl, and lower heteroalkyl, any of which may be optionally substituted. Additionally, the R and R’ of a lower amino group may combine to form a five- or six-membered heterocycloalkyl, either of which may be optionally substituted.
- oxy or “oxa,” as used herein, alone or in combination, refer to –O–.
- partially unsaturated as used herein, alone or in combination, refers to a straight-chain, branched-chain or ring moiety that includes at least one double or triple bond and that is not fully saturated.
- partially unsaturated when used in reference to a ring moiety means a ring having one or multiple sites of unsaturation but does not include aryl rings or heteroaryl rings as defined herein.
- ring member atoms refers to all of the atoms that form the covalent structure of a cyclic ring structure. By “saturated” is meant that the carbon-containing group contains no carbon-carbon double or triple bonds.
- a composition includes a pharmaceutically acceptable salt of a compound herein.
- pharmaceutically acceptable salts include carboxylate salts, amino acid addition salts and zwitterionic forms thereof, which are known to those skilled in the art as suitable for use with humans and animals. (See, e.g., Gerge, S. M., et al, "Pharmaceutical Salts," Pharm. Sci. (1977) 66:1-19).
- a composition in cases where a compound is sufficiently basic or acidic to form a stable nontoxic acid or base salt, a composition includes a pharmaceutically acceptable salt of the compound.
- pharmaceutically acceptable salts are organic acid addition salts formed with acids that form a physiological acceptable anion, non-limiting examples of which include tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, [alpha]-ketoglutarate, and [alpha]- glycerophosphate.
- Suitable inorganic salts may also be formed, including hydrochloride, sulfate, nitrate, bicarbonate, and carbonate salts.
- compositions can include an isomer of a compound herein.
- isomers are stereoisomers (e.g., diastereomers and enantiomers) and structural isomers such as tautomers.
- a composition can include a mixture containing two or more isomers of a compound herein.
- a mixture can include an isomer that predominates over one or more other isomers of a compound herein (e.g., the molar amount of one isomer may represent about 55% or more of all isomers of the compound (e.g., about 60% or more, about 65% or more, about 70% or more, about 75% or more, about 80% or more, about 85% or more)).
- a composition can include an isomerically pure form of a compound herein, in which the molar amount of one isomer can represent about 95% or more (e.g., about 96% or more, about 97% or more, about 98% or more, about 99% or more or about 99.5% or more) of all isomers of the compound.
- a compound in a composition provided herein is isolated (e.g., isolated from other types of molecules).
- a composition containing a compound described herein sometimes is at least about 80% pure, by weight, and sometime is at least about 85% pure, at least about 90% pure, at least about 95% pure, at least about 99% pure, or at least about 99.5% pure.
- a composition containing a compound described herein that is 90% pure contains 90% by weight of the compound described and 10% by weight of components other than the compound described.
- a composition can contain a compound herein.
- a compound in a composition can inhibit an activity of a protein kinase (PK; for example, a PK polypeptide).
- PK activity can include a PK binding activity (for example, binding of a PK to a substrate that the PK phosphorylates and/or binding of a PK to a binding partner polypeptide that the PK does not phosphorylate) and/or PK catalytic activity (for example, PK substrate phosphorylation activity).
- a compound herein is capable of effectively inhibiting, moderately inhibiting and/or selectively inhibiting a PK activity.
- a composition containing a compound herein can be for inhibition of a PK activity, inhibition of an activity of two or more PKs, preparation of a medicament and/or for preparation of a treatment of a PK-associated condition.
- a compound in a composition is or has been isolated (for example, isolated from other types of molecules).
- a compound sometimes is at least about 80% pure, by weight, in a composition and sometime is at least about 85% pure, at least about 90% pure, at least about 95% pure, at least about 99% pure, or at least about 99.5% pure.
- a compound that is 90% pure in a composition contains 90% by weight of the compound and 10% by weight of components other than the compound.
- a composition containing a compound herein can be a pharmaceutical composition.
- a pharmaceutical composition can include a compound herein as an active ingredient and one or more pharmaceutically acceptable additives, including one or more pharmaceutically acceptable excipients.
- One or more pharmaceutically acceptable excipients in a pharmaceutical composition typically form a carrier for the active ingredient.
- Non-limiting examples of excipient additives include a pharmaceutically acceptable solvent, diluent, isotonic agent, buffering agent, stabilizer, preservative, antioxidant, vasoconstrictive agent, antibacterial agent, antifungal agent, adsorption delaying agent, sustained release agent (for example, for example, U.S. Patent No.5,624,677), and the like.
- One or more additives can be combined with an active ingredient for the manufacture of a pharmaceutical composition by a method known in the art.
- a pharmaceutical composition sometimes is prepared as a solid (for example, powder) or liquid (for example, aqueous solution, emulsion (for example, micro-emulsion, nano-emulsion)).
- Non-limiting examples of solvents and diluents include water, saline, dextrose, ethanol, glycerol, oil, water-miscible organic cosolvents such as acetone or dimethyl sulfoxide (DMSO), and the like.
- Non-limiting examples of isotonic agents include sodium chloride, dextrose, mannitol, glucose, sucrose, sorbitol, lactose, and the like.
- Non-limiting examples of buffering agents include bicarbonate, phosphate, and the like. Phosphate-buffered saline (PBS), which may be buffered to provide a neutral pH, or in certain embodiments an acidic pH, sometimes is utilized.
- PBS Phosphate-buffered saline
- Non-limiting examples of stabilizers include gelatin, albumin, and the like.
- Non-limiting examples of a preservatives include gentamicin, merthiolate, chlorocresol and the like.
- Water or saline, when used for preparing a pharmaceutical composition, may be buffered or not buffered.
- Non-limiting examples of saline solutions that can be used to prepare a pharmaceutical composition include lactated Ringer's solution, acetated Ringer's solution, intravenous sugar solutions (for example, 5% dextrose in normal saline (D5NS), 10% dextrose in normal saline (D10NS), 5% dextrose in half-normal saline (D5HNS) and 10% dextrose in half-normal saline (D10HNS)).
- D5NS normal saline
- D10NS 5% dextrose in normal saline
- D10NS 5% dextrose in normal saline
- D5HNS 5% dextrose in half-normal saline
- D10HNS 10% dextrose in half-normal saline
- buffered saline solutions and related solutions include phosphate buffered saline (PBS), TRIS-buffered saline (TBS), Hank's balanced salt solution (HBSS), Earle's balanced salt solution (EBSS), standard saline citrate (SSC), HEPES-buffered saline (HBS), and Gey's balanced salt solution (GBSS).
- PBS phosphate buffered saline
- HBSS Hank's balanced salt solution
- EBSS Earle's balanced salt solution
- SSC standard saline citrate
- HBS HEPES-buffered saline
- GBSS Gey's balanced salt solution
- an additive enhances solubility and/or bioavailability of an active ingredient.
- a solubility-enhancing additive may include one or more of: a lipid, polyethylene glycol (PEG), polysorbate, glycerol, glycerin, dimethylacetamide, triacetin, an oil (for example, a vegetable oil), or combination thereof.
- solubility of an active ingredient is characterized by a particular amount of excipient that confers solubility to the active ingredient.
- Any suitable antioxidant can be included in a pharmaceutical composition, non-limiting examples of which include (1) butylated hydroxytoluene (BHT), (2) butylated hydroxyanisole (BHA), (3) DL- alpha-tocopherol, (4) ascorbyl palmitate and (5) propyl gallate.
- a pharmaceutical composition can include a mixture of two, three, four or five antioxidants.
- a concentration of an active ingredient in a liquid composition sometimes is from about 0.1 wt% to about 35 wt%, or sometimes from about 0.5 wt% to about 10 wt%.
- the concentration in a semi- solid or solid composition such as a gel or a powder sometimes is about 0.1 wt% to about 5 wt%, or sometimes about 0.5 wt% to about 2.5 wt%. Higher concentrations are also appropriate for some solid or semi-solid compositions and may include amounts up to about 25 wt% or up to about 50 wt% or more.
- a pharmaceutical composition may be prepared according to conventional techniques known in the pharmaceutical industry.
- such techniques include bringing an active ingredient into association with on or more pharmaceutical carrier(s) and/or excipient(s) in liquid form or finely divided solid form, or both, and then shaping the product if required.
- a pharmaceutical composition may be incorporated into a suitable dosage form (for example, unit dosage form), non-limiting examples of which include a tablet, capsule, gel capsule, liquid syrup, soft gel, suppository, enema, dressing or device (for example, in a syringe (for example, auto- injection device) or microneedle device).
- a pharmaceutical composition may be formulated as a suspension in aqueous, non-aqueous, or mixed media.
- Aqueous suspensions may further contain substances that increase viscosity, including for example, sodium carboxymethylcellulose, sorbitol, and/or dextran.
- a suspension may also contain one or more stabilizers.
- An amount of active ingredient required for use in treatment will vary not only with the particular form selected (for example, the salt selected) but also with route of administration, the nature of the condition being treated and the age and condition of the patient and ultimately will be at the discretion of the attendant physician or clinician. Any additive and material used in preparing a unit dosage form typically is pharmaceutically acceptable and substantially non-toxic in the amounts employed.
- a composition can include a pharmaceutically acceptable ester or amide of a compound herein.
- a composition includes a pharmaceutically acceptable salt of a compound herein.
- Non-limiting examples of pharmaceutically acceptable salts include carboxylate salts, amino acid addition salts and zwitterionic forms thereof, which are known to those skilled in the art as suitable for use with humans and animals. (See, for example, Gerge, S. M., et al, "Pharmaceutical Salts,” Pharm. Sci. (1977) 66:1-19).
- a composition includes a pharmaceutically acceptable salt of the compound.
- Non-limiting examples of pharmaceutically acceptable salts are organic acid addition salts formed with acids that form a physiological acceptable anion, non-limiting examples of which include tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, [alpha]-ketoglutarate, and [alpha]-glycerophosphate.
- Suitable inorganic salts may also be formed, including hydrochloride, sulfate, nitrate, bicarbonate, and carbonate salts.
- Pharmaceutically acceptable salts are obtained using standard procedures known in the art. For example, pharmaceutically acceptable salts may be obtained by reacting a sufficiently basic compound with a suitable acid affording a physiologically acceptable anion.
- a composition can include an isomer of a compound herein.
- isomers are stereoisomers (e.g., diastereomers and enantiomers) and structural isomers such as tautomers.
- a composition can include a mixture containing two or more isomers of a compound herein.
- a mixture can include an isomer that predominates over one or more other isomers of a compound herein (e.g., the molar amount of one isomer may represent about 55% or more of all isomers of the compound (e.g., about 60% or more, about 65% or more, about 70% or more, about 75% or more, about 80% or more, about 85% or more)).
- a composition can include an isomerically pure form of a compound herein, in which the molar amount of one isomer can represent about 95% or more (e.g., about 96% or more, about 97% or more, about 98% or more, about 99% or more or about 99.5% or more) of all isomers of the compound.
- compositions for oral administration A pharmaceutical composition may be provided as a tablet (for example, ingestible tablet, buccal tablet), troche, capsule (for example, hard- or soft-shell gelatin capsule), drink, elixir, suspension, syrup, wafer, and the like, and/or may be incorporated directly in food or drink that is part of a subject’s diet. Such compositions and preparations sometimes contain at least 0.1% of active ingredient. The percentage of the compositions and preparations may be varied and sometimes are about 2% to about 60% of the weight of a given unit dosage form. The amount of active ingredient in a pharmaceutical composition is such that an effective dosage level can be obtained.
- Tablets, troches, pills, capsules, and the like may contain one or more of the following: a binder such as gum tragacanth, acacia, corn starch or gelatin; an excipient such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; a sweetening agent such as sucrose, fructose, lactose or aspartame; a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring.
- a binder such as gum tragacanth, acacia, corn starch or gelatin
- an excipient such as dicalcium phosphate
- a disintegrating agent such as corn starch, potato starch, alginic acid and the like
- a lubricant such as magnesium stearate
- a sweetening agent such as sucrose, fructose, lactose or aspartame
- compositions for topical administration For topical administration, a compound herein may be applied in liquid form.
- a compound herein may be combined with a dermatologically acceptable carrier, which may be a solid or a liquid.
- a compound herein may be formulated with a solid carrier, which include finely divided solids such as talc, clay, microcrystalline cellulose, silica, alumina and the like.
- Useful liquid carriers include water, alcohols or glycols or water-alcohol/glycol blends, or phospholipids in propylene glycol/ethylene glycol, in which the a compound herein can be dissolved or dispersed at an effective level, optionally with the aid of non-toxic surfactants.
- a composition sometimes includes a diluent and sometimes a carrier (for example, assimilable, editable), buffer, preservative and the like. Additives such as fragrances and additional antimicrobial agents can be added to optimize the properties for a given use.
- a liquid composition can be applied from an absorbent pad, used to impregnate a bandage or other dressing, or sprayed onto the affected area using a pump-type or aerosol sprayer.
- a thickener such as a synthetic polymer, fatty acid, fatty acid salt and/or ester, fatty alcohol, modified cellulose or modified mineral material, can also be employed with a liquid carrier to form a spreadable cream, paste, gel, ointment, soap, and the like, for application directly to the skin of a subject.
- a pharmaceutical composition suitable for injection can include a sterile aqueous solution or dispersion or sterile powder for the extemporaneous preparation of a sterile injectable solution or dispersion.
- An injectable formulation often is sterile and often is fluid. It typically is stable under the conditions of manufacture and storage and typically is preserved against contaminating microorganisms, such as bacteria and fungi.
- a pharmaceutical composition can be delivered to a subject via any suitable injection device, including without limitation, a syringe, needle or microneedle (for example, including a syringe device for self-administration; auto-injection device).
- An injectable formulation sometimes includes a carrier, which can be a solvent, excipient, or dispersion medium.
- a liquid carrier or vehicle can be a solvent or liquid dispersion medium including, for example, water, ethanol, a polyol (for example, glycerol, propylene glycol, liquid polyethylene glycols, and the like), vegetable oil, nontoxic glyceryl ester, or suitable mixture thereof.
- Fluidity of an injectable formulation can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of a surfactant.
- Prevention of the action of microorganisms can be affected by an antibacterial and/or antifungal agent, for example, paraben, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
- an isotonic agent may be included, for example, a sugar or sodium chloride.
- Prolonged absorption of an injectable composition can be affected by use of an absorption delaying agent, for example, aluminum monostearate and/or gelatin.
- a pharmaceutical composition may include a co-polymer such as, for example, a co-polymer selected from poly(vinyl alcohol), poly(vinyl pyrrolidone), and hypromellose acetate succinate.
- a sterile injectable solution can be prepared by incorporating an active ingredient in the required amount in the appropriate solvent with one or more other ingredients, as required, followed by filter sterilization.
- methods of preparation include vacuum drying and freeze-drying techniques, which yield a powder including the active ingredient and any additional desired ingredient present in the previously sterile-filtered solution.
- Protein kinase inhibition A compound can be an inhibitor of one or more protein kinases (PKs), and can be used to inhibit one or more PKs.
- PKs protein kinases
- a compound that inhibits a PK can bind to a PK, inhibit PK substrate phosphorylation activity and/or inhibit binding activity of a PK to another entity (for example, a polypeptide to which the PK binds).
- a compound that is an inhibitor of one or more PKs sometimes is an effective inhibitor, moderate inhibitor, mild inhibitor and/or ineffective inhibitor of one or more PKs.
- a compound is designated as an “effective inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by greater than 90%; and/or (ii) the compound inhibits PK activity at a measured IC 50 value of less than 20 nM.
- a compound is designated as a “moderate inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by 70% to 90%; and/or (ii) the compound inhibits PK activity at a measured IC50 value between 20 nM and 40 nM.
- a compound is designated as a “mild inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by 30% to 70%; and/or (ii) the compound inhibits PK activity at a measured IC50 value between 40 nM and 200 nM.
- a compound is designated as an “ineffective inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by less than 30%; and/or (ii) the compound inhibits PK phosphorylation at a measured IC50 value of greater than 200 nM.
- An “effective inhibitor” can be used to effectively inhibit a PK
- a “moderate inhibitor” can be used to moderately inhibit a PK
- a “mild inhibitor” can be used to mildly inhibit a PK
- an “ineffective inhibitor” can be used to ineffectively inhibit or not inhibit a PK.
- An IC50 value or percent activity can be measured by a suitable assay, such as an in vitro assay that assesses PK phosphorylation activity or PK ligand binding, for example.
- PK inhibition is assessed according to an IC50 value or percent activity measured by a peptide cleavage assay, tracer displacement assay, solid phase inhibitor competition assay, ADP formation assay, as described herein (described in Example 9), for example.
- a compound that contains a quinazolinyl group and an amine-linked phenyl group can be used to inhibit one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound that contains a quinazolinyl group and an amine-linked phenyl group can selectively inhibit a JAK2 PK.
- the compound effectively inhibits or moderately inhibits a JAK2(wt) PK and does not effectively inhibit and does not moderately inhibit a JAK1(wt) PK (for example, the compound mildly inhibits or ineffectively inhibits a JAK1 PK).
- the compound inhibits JAK3(wt) PK, and optionally effectively inhibits JAK3(wt) PK, or optionally moderately inhibits a JAK3(wt) PK.
- the compound inhibits, and optionally effectively inhibits, one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound effectively inhibits two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, SRC family PK, DDR family PK, and/or PTK family PK.
- the compound moderately inhibits two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound that effectively inhibits and/or optionally moderately inhibits a PK in one or more of the foregoing PK families does not effectively inhibit, and/or does not moderately inhibit, one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound used to inhibit a PK is a compound herein (in Table A, for example).
- a composition used to inhibit a PK contains a compound herein (in Table A, for example).
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an ABL family PK, including an ABL1 PK, including ABL1(wt) and/or one or more ABL1 variants; and/or an ABL2 PK, including ABL2(wt) and/or one or more ABL2 variants.
- An ABL1 variant can include one or more of the following amino acid substitutions (relative to ABL1(wt)): T315I, G250E, Q252H, Y253F, E255K, F317L, M351T and H396P, and/or other ABL1 amino acid substitution described herein.
- An ABL2 PK also is referred to as an ARG PK.
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a BTK family PK.
- a BTK family PK can include: a BTK PK, including BTK(wt) and/or one or more BTK variants; a BMX PK, including BMX(wt) and/or one or more BMX variants; an ITK PK, including ITK(wt) and/or one or more ITK variants; a TEC PK, including TEC(wt) and/or one or more TEC variants; and a TXK PK, including TXK(wt) and/or one or more TXK variants.
- BMX is referred to also as ETK
- ITK is referred to also as EMT
- TXK is referred to also as RLK.
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an Aurora (AURK) family PK.
- An AURK family PK can include: an AURKA PK, including AURKA(wt) and/or one or more AURKA variants; an AURKB PK, including AURKB(wt) and/or one or more AURKB variants; and an AURKC PK, including AURKC(wt) and/or one or more AURKC variants.
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a JAK family PK.
- a JAK family PK can include: a JAK1 PK, including JAK1(wt) and/or one or more JAK1 variants; a JAK2 PK, including JAK2(wt) and/or one or more JAK2 variants; a JAK3 PK including JAK3(wt) and/or one or more JAK3 variants; and a TYK family PK.
- a TYK family PK can be a TYK2 family PK, including TYK2(wt) and/or one or more TYK2 variants.
- a JAK2 PK variant can include the amino acid substitution V617F, relative to JAK2(wt).
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a TYK2 family PK and sometimes is a Subgroup 2 compound.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a TRK family PK.
- a TRK family PK can include: a TRKA PK, including TRKA(wt) and/or one or more TRKA variants; a TRKB PK, including TRKB(wt) and/or one or more TRKB variants; a TRKC PK, including TRKC(wt) and/or one or more TRKC variants; and a ROS1 PK, including ROS1(wt) and/or one or more ROS1 variants.
- TRKA is referred to also as NTRK1
- TRKB is referred to also as NTRK2
- TRKC is referred to also as NTRK3.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an EPH family PK.
- An EPH family PK can include an EPHA1 PK, including EPHA1(wt) and/or one or more EPHA1 variants; an EPHA2 PK, including EPHA2(wt) and/or one or more EPHA2 variants; an EPHA5 PK, including EPHA5(wt) and/or one or more EPHA5 variants; an EPHA8 PK, including EPHA8(wt) and/or one or more EPHA8 variants; an EPHB1 PK, including EPHB1(wt) and/or one or more EPHB1 variants; and/or an EPHB2 PK, including EPHB2(wt) and/or one or more EPHB2 variants.
- a TNK family PK can include a TNK1 PK, including TNK1(wt) and/or one or more TNK1 variants; and/or a TNK2 PK, including TNK2(wt) and/or one or more TNK2 variants.
- a TNK2 PK sometimes is referred to as an ACK PK.
- a PTK family PK can include a PTK2B PK, including PTK2B(wt) and/or one or more PTK2B variants.
- a PTK2B PK can be referred to as a FAK2 PK.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a SRC family PK.
- a SRC family PK can include a SRC(wt) and/or one or more SRC variants, and a SRC-N1(wt) and/or one or more SRC-N1 variants.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a LCK family PK.
- a LCK family PK can include a LCK(wt) and/or one or more LCK variants.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a DDR family PK.
- a DDR family PK can include a DDR2 PK, including DDR2(wt) and/or one or more DDR2 variants.
- a DDR variant PK can include a T654M and/or N456S amino acid substitution.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a PLK family PK.
- a PLK family PK can include PLK4(wt) and/or one or more PLK4 variants.
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a PLK4 family PK and sometimes is a Subgroup 3 compound.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an IRAK family PK.
- An IRAK family PK can include an IRAK1 PK, including IRAK1(wt) and/or one or more IRAK1 variants; and/or an IRAK3 PK, including IRAK3(wt) and/or one or more IRAK3 variants.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a RET family PK.
- a RET family PK can include: a RET PK, including RET(wt) and/or one or more RET variants.
- a RET variant can include one or more of the following amino acid substitutions, relative to RET(wt): A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F.
- a compound that inhibits a RET family PK sometimes also inhibits BMX, BTK, TXK, JAK1, JAK2, JAK3, TRKA, TRKB, TRKC, AURKA, an EPH family PK, IRAK3 and PLK4.
- a compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a RET family PK and the compound sometimes is a Subgroup 2 compound.
- a compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, one or more, or two or more, variants of a PK.
- a compound is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, one or more of the following PK variants: (i) an ABL1 variant optionally containing one or more of the following amino acid substitutions relative to ABL1(wt): T315I, G250E, Q252H, Y253F, E255K, F317L, M351T and H396P; (ii) a JAK2 PK variant optionally containing the amino acid substitution V617F relative to JAK2(wt); (iii) a RET variant optionally containing one or more of the following amino acid substitutions relative to RET(wt): A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F; and/or (iv)
- a PK variant can be referred to with the PK name as a prefix and an amino acid substation as a suffix, where the amino acid substation suffix is separated from the PK name prefix by a hyphen (for example, ABL1-T315I or DDR2-N456S) or by parentheses (for example, ABL1(T315I) or DDR2(N456S)).
- a hyphen for example, ABL1-T315I or DDR2-N456S
- parentheses for example, ABL1(T315I) or DDR2(N456S
- a compound can be an effective inhibitor of, and can be used to inhibit, two or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound can be an effective inhibitor of, and can be used to inhibit, an ABL family PK and a BTK family PK (for example, a BTK(wt) PK).
- a compound can be an effective inhibitor of, and can be used to inhibit, an ABL family PK and a AURK family PK.
- a compound can be an effective inhibitor of, and can be used to inhibit, an ABL family PK and a JAK family PK (for example, JAK2(wt) and/or JAK2(V617F)).
- a compound can be an effective inhibitor of, and can be used to inhibit, three or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound can be an effective inhibitor of an ABL family PK (for example, ABL1(wt) and/or ABL1(T315I)), a BTK family PK (for example, a BTK(wt) PK) and a AURK family PK, for example.
- ABL family PK for example, ABL1(wt) and/or ABL1(T315I)
- BTK family PK for example, a BTK(wt) PK
- AURK family PK for example.
- a compound can be an effective inhibitor of, and can be used to inhibit, four or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a compound can be an effective inhibitor of: an ABL family PK (for example, ABL1(wt) and/or ABL1(T315I)), a BTK family PK (for example, a BTK(wt) PK), a AURK family PK, and a JAK family PK.
- ABL family PK for example, ABL1(wt) and/or ABL1(T315I)
- BTK family PK for example, a BTK(wt) PK
- AURK family PK for example, a JAK family PK.
- a compound can be an effective inhibitor of: an ABL family PK (for example, ABL1(wt) and/or ABL1(T315I)), a BTK family PK (for example, a BTK(wt) PK), a AURK family PK, a JAK family PK (for example, JAK2(wt) PK and/or JAK2 variant PK containing a V617F amino acid substitution), and a TRK family PK.
- ABL family PK for example, ABL1(wt) and/or ABL1(T315I
- BTK family PK for example, a BTK(wt) PK
- AURK family PK for example, a JAK family PK (for example, JAK2(wt) PK and/or JAK2 variant PK containing a V617F amino acid substitution)
- TRK family PK for example, TRK family PK (for example, ABL1(wt) and/or ABL1(T
- a compound can be an effective inhibitor of, and can be used to inhibit, five of, or six of, or seven of, or eight of, or nine of, or ten of, or eleven of, or twelve of, or thirteen of or all of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK, and can be a Subgroup 1 compound.
- a compound of Subgroup 1 can be an effective inhibitor of, or optionally a moderate inhibitor of, and can be used to inhibit, multiple PTKs, including ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or all of an ABL family PK, a BTK family PK, an AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a DDR family PK, and/or a PTK family PK.
- a compound can inhibit a homo sapiens PK or viral PK.
- a polypeptide of each of the foregoing wild type (wt) homo sapiens PKs is accessible in (i) a public database (World Wide Web URL ncbi.nlm.nih.gov/protein/) according to the corresponding accession number having a “NP” or “AA” prefix, and (ii) a public database (World Wide Web URL uniprot.org/uniprotkb/) according to the corresponding accession number having a “P” prefix, in Table 4 of Example 9.
- a polypeptide of a corresponding PK variant can be determined according to the wt polypeptide accessed from the database and the position of one or more amino acid substitutions designated.
- JAK1(wt), JAK2(wt) and JAK3(wt) are receptor PKs.
- the JAK1(wt) catalytic domain includes amino acids 866-1154 of the JAK1(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the JAK2(wt) catalytic domain includes amino acids 808-1132 of the JAK2(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the JAK3(wt) catalytic domain includes amino acids 781-1124 of the JAK3(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- TRKA(wt), TRKB(wt) and TRKC(wt) also are receptor PKs.
- the TRKA(wt) catalytic domain includes amino acids 441-796 of the TRKA(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the TRKB(wt) catalytic domain includes amino acids 526-838 of the TRKB(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the TRKC(wt) catalytic domain includes amino acids 510-825 of the TRKC(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- RET(wt) also is a receptor PK and the catalytic domain includes amino acids 658-1114 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- EPHA1(wt), EPHA2(wt), EPHA5(wt), EPHA8(wt), EPHB1(wt) and EPHB2(wt) PKs also are receptor PKs.
- the EPHA1(wt) catalytic domain includes amino acids 568-976 of the EPHA1(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the EPHA2(wt) catalytic domain includes amino acids 560-976 of the EPHA2(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the EPHA5(wt) catalytic domain includes amino acids 595-1037 of the EPHA5(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the EPHA8(wt) catalytic domain includes amino acids 565-1005 of the EPHA8(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the EPHB1(wt) catalytic domain includes amino acids 612-887 of the EPHB1(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the EPHB2(wt) catalytic domain includes amino acids 616-884 of the EPHB2(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- TYK2(wt) also is a receptor PK and the catalytic domain includes amino acids 833-1187 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- TNK2(wt) which also is referred to as ACK
- ACK also is a receptor PK and the catalytic domain includes amino acids 110-476 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- IRAK1(wt) also is a receptor PK and the catalytic domain includes amino acids 194-712 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- DDR2 also is a receptor PK and the catalytic domain includes amino acids 422-855 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays.
- the SRC(wt) polypeptide can be accessed by either of the accession numbers shown in Table 4 of Example 9.
- the SRC-N1(wt) polypeptide is nearly identical to the SRC(wt) polypeptide but includes a 6-amino acid polypeptide insertion in the SH3 domain of the SRC(wt) polypeptide.
- the T at position 117 in the SRC(wt) polypeptide is replaced by TRKVDVR in the SRC-N1(wt) polypeptide.
- a PK referred to as having an amino acid substitution herein typically includes the designated amino acid substitution at the designated position in the polypeptide accessed by the accession number referenced in Table 4 of Example 9, and can be the length of the accessed polypeptide, or a portion thereof containing (i) a catalytic domain or (ii) a fragment of a catalytic domain having phosphoryl-transfer activity (for example, in vitro phosphoryl-transfer activity).
- ABL1 inhibition In certain embodiments, a compound is an effective inhibitor or moderate inhibitor of one or more, or two or more, ABL1 variant polypeptides. Such a compound can be an effective inhibitor or moderate inhibitor of ABL1(wt).
- a compound that is an effective inhibitor or two or more ABL1 variant polypeptides can be considered a pan-ABL1 inhibitor.
- a compound is an effective inhibitor of two or more ABL1 variant polypeptides containing one or more of M244V, G250E, Q252H, Y253F, Y253H, E255K, E255V, V299L, F311L, T315A, T315I, F317L, F317V, M351T, E355G, F359V, V379I, L387M, H396P and/or H396R.
- a compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of one or more other ABL1 variant polypeptides (for example, two or more other ABL1 variant polypeptides, three or more other ABL1 variant polypeptides, or four or more other ABL1 variant polypeptides).
- a compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of one or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L).
- a compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of two or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L).
- a compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of three or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L).
- a compound sometimes is an effective inhibitor of ABL1(T315I), an effective inhibitor one or more other ABL1 variant polypeptides, and a moderate inhibitor of one or more other ABL1 variant polypeptides.
- a compound sometimes is an effective inhibitor of ABL1(T315I), an effective inhibitor of one or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L), and a moderate inhibitor of one or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L).
- a compound sometimes is an effective inhibitor of ABL1(T315I), ABL1(G250E), ABL1(Y253F) and ABL1(E255K), and a moderate inhibitor of ABL1(F317L).
- ABL1(wt) and ABL1 variant polypeptides are described in greater detail hereafter.
- isoform a Two common alternatively spliced isoforms of the homo sapiens ABL1 PTK are referred to herein as "isoform a" and “isoform b.”
- the ABL1 "isoform a" polypeptide N- terminal region underlined above by single underlining differs from the ABL1 "isoform b" polypeptide N-terminal region underlined above by single underlining.
- the adjacent, downstream polypeptide region in each of the ABL1 "isoform a” polypeptide and ABL1 "isoform b" polypeptide, which is not underlined with single underlining, and which starts from the end of the N-terminal region underlined by single underlining and ends at the C-terminus, is identical (the "identical portion").
- An ABL1 polypeptide referred to as an "ABL1 wild type" polypeptide can (1) contain the polypeptide of SEQ ID NO:3; or (2) contain the polypeptide of SEQ ID NO:1; or (3) contain the polypeptide of SEQ ID NO:2; or (4) contain the polypeptide of SEQ ID NO:3 and: (i) an adjacent N- terminal region containing 2 or more contiguous amino acids in the double-underlined region and/or single underlined region shown above in SEQ ID NO:1 or SEQ ID NO:2, or (ii) an adjacent C- terminal region containing 2 or more contiguous amino acids in the hatched-underlined region shown above in SEQ ID NO:1 and SEQ ID NO:2, or a combination of (i) and (ii); or (5) contain a fragment of (1), (2), (3) or (4) containing 25 or more contiguous amino acids or 1100 or fewer contiguous amino acids; or (6) contain an ABL1 polypeptide portion
- An ABL1(wt) polypeptide typically does not include a substitution of an amino acid in the identical portion, i.e., the portion of the ABL1 "isoform a" and "isoform b" polypeptides above not underlined by single-underlining.
- An ABL1(wt) polypeptide typically includes no amino acid insertion or amino acid deletion relative to the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3.
- a fragment sometimes includes 25 or more contiguous amino acids of the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 (for example, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 65 or more, 70 or more, 75 or more, 80 or more, 85 or more, 90 or more, 95 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more, 190 or more, 200 or more, 225 or more, 250 or more, 275 or more, 300 or more, 325 or more, 350 or more, 375 or more, 400 or more, 425 or more, 450 or more, 475 or more, 500 or more, 525 or more, 550 or more, 575 or more, 600 or more, 625 or more, 650 or more, 675 or more, 700 or more, 725 or more, 750 or more, 775 or more, 800 or more
- a fragment sometimes includes 1100 or fewer contiguous amino acids of the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 (for example, 50 or fewer, 55 or fewer, 60 or fewer, 65 or fewer, 70 or fewer, 75 or fewer, 80 or fewer, 85 or fewer, 90 or fewer, 95 or fewer, 100 or fewer, 110 or fewer, 120 or fewer, 130 or fewer, 140 or fewer, 150 or fewer, 160 or fewer, 170 or fewer, 180 or fewer, 190 or fewer, 200 or fewer, 225 or fewer, 250 or fewer, 275 or fewer, 300 or fewer, 325 or fewer, 350 or fewer, 375 or fewer, 400 or fewer, 425 or fewer, 450 or fewer, 475 or fewer, 500 or fewer, 525 or fewer, 550 or fewer, 575 or fewer, 600 or fewer, 625 or fewer, 650 or fewer, 675
- a non-ABL1 polypeptide portion present in an ABL1(wt) polypeptide sometime is (i) an N-terminal portion, or is located closer to the N-terminus of the ABL1(wt) polypeptide than the ABL1 polypeptide portion; or (ii) a C-terminal portion, or is located closer to the C-terminus of the ABL1(wt) polypeptide than the ABL1 polypeptide portion; or (iii) a combination of (i) and (ii) where there are multiple non-ABL1 polypeptide portions.
- a non-ABL1 polypeptide portion present in an ABL1(wt) polypeptide sometimes contains a BCR portion (for example, a BCR portion of a BCR- ABL1 fusion polypeptide identified in cancer patients).
- a BCR portion present in an ABL1(wt) polypeptide can be an N-terminal portion, or can be located closer to the N-terminus of the ABL1(wt) polypeptide than the ABL1 polypeptide portion.
- An ABL1(wt) polypeptide can be modified with one or more components that facilitate use of the polypeptide, including without limitation one or more of separating, purifying, isolating and detecting an ABL1 polypeptide, and measuring an activity of an ABL1 polypeptide (for example, binding activity of an ABL1 polypeptide to a test compound and/or binding agent; phosphorylation activity of an ABL1 polypeptide).
- an ABL1(wt) polypeptide can be modified to include a binding pair member (for example, biotin/avidin (or streptavidin), antibody/antigen), a luminescence molecule (for example, bioluminescence molecule; luciferase or portion thereof; nano-luciferase), fluorophore (for example, member or members of a fluorescence resonance energy transfer (FRET) pair), dye, particle (for example, nanoparticle), and the like, for example.
- a binding pair member for example, biotin/avidin (or streptavidin), antibody/antigen
- a luminescence molecule for example, bioluminescence molecule; luciferase or portion thereof; nano-luciferase
- fluorophore for example, member or members of a fluorescence resonance energy transfer (FRET) pair
- dye for example, nanoparticle
- particle for example, nanoparticle
- a non-ABL1 polypeptide portion is an N-terminal or C-terminal portion useful to immobilizing the ABL1 polypeptide to a solid phase.
- a non-ABL polypeptide portion contains a poly-histidine peptide portion (for example, a peptide containing 5-20, or 6-10, consecutive histidine amino acids) capable of associating with a transition metal-containing solid phase (for example, a solid phase containing Mn, Fe, Co, Ni or Cu).
- a non-ABL1 polypeptide portion sometimes contains one or both of a linker polypeptide portion and a cleavage recognition polypeptide portion. Multiple linker polypeptide portions are known and can be selected.
- cleavage recognition polypeptide portions also are known and can be selected for cleavage of an N-terminal portion or C-terminal portion from an ABL1 polypeptide under suitable cleavage conditions.
- a non-limiting example of an ABL1(wt) polypeptide containing the "isoform a" polypeptide of SEQ ID NO:1 and a non-ABL1 C-terminal portion (highlighted in bold text) containing a poly-histidine peptide portion and linker portion, referred to herein as "isoahABL1(wt),” is as follows (SEQ ID NO:4): MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPN LFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWY HGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRV
- the "isoblABL1(wt)" polypeptide can be utilized in a labeled peptide competition assay, such as a bioluminescence resonance energy transfer (BRET) intracellular assay (for example, Machleidt et al., ACS Chem. Biol.10:1797-1804 (2015)), for example.
- An ABL1 polypeptide referred to herein as an "ABL1 variant polypeptide” typically includes one or more amino acid substitutions relative to an ABL1(wt) polypeptide.
- An ABL1 variant polypeptide may include a structure described herein for an ABL1(wt) polypeptide, with the exception that the variant polypeptide includes one or more amino acid substitutions relative to the ABL1(wt) polypeptide.
- An ABL1 variant polypeptide sometimes includes up to ten amino acid substitutions relative to an ABL1(wt) polypeptide (for example, substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids relative to an ABL1(wt) polypeptide).
- An amino acid substitution in an ABL1 variant polypeptide is defined herein relative to a position in SEQ ID NO:1, by the following notation utilizing the one-letter amino acid code: amino acid in SEQ ID NO:1 - at position in SEQ ID NO:1 - corresponding substituted amino acid in ABL1 variant polypeptide.
- amino acid substitution notated as "T315I” refers to the threonine at position 315 in SEQ ID NO:1 substituted by isoleucine in an ABL1 variant ("ABL1(T315I)").
- An ABL1 variant polypeptide can include an amino acid substitution corresponding to a position in SEQ ID NO:1 in instances where the ABL1 variant polypeptide includes the same number, or does not include the same number, of amino acids of the polypeptide of SEQ ID NO:1.
- a corresponding amino acid position of an amino acid substitution can be readily determined for a particular ABL1 variant polypeptide as known in the art.
- URL World Wide Web Uniform Resource Locator
- SEQ ID NO:3 corresponds to threonine 315 in SEQ ID NO:1.
- An ABL1 variant polypeptide often includes no amino acid insertion or amino acid deletion relative to the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3.
- An ABL1 variant polypeptide can, in certain instances, include (i) an amino acid insertion within the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 containing 1, 2 or 3 contiguous amino acids; or (ii) an amino acid deletion of 1, 2 or 3 contiguous amino acids in the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3; or a combination of (i) and (ii).
- An ABL1 variant polypeptide may include an amino acid substitution in a particular portion of the polypeptide, non-limiting examples of which include a p-loop portion, SH3 contact portion, SH2 contact portion and A-loop portion.
- amino acid substitutions any one or more of which may be present in an ABL1 variant polypeptide, are illustrated in FIG.2 (Soverini et al., Blood 118(5):1208-1215 (2011)).
- An ABL1 variant may include one or more of the following amino acid substitutions: M237V, I242T, M244V, K247R, L248V, G250E, G250R, Q252R, Q252H, Y253F, Y253H, E255K, E255V, E258D, W261L, L273M, E275K, E275Q, D276G, T277A, E279K, V280A, V289A, V289I, E292V, E292Q, I293V, L298V, V299L, F311L, F311I, T315A, T315I, F317L, F317V, F317I, F317C, Y320C, L324Q, Y342H, M343T, A344V, A350V, M351T, E355D, E355G, E355A, F359V, F
- substitutions F317L and V299L have been reported to impart dasatinib therapy resistance and substitutions Y253H, E255K, E255V, F359V and F359C have been reported to impart nilotinib therapy resistance.
- substitution T315I has been reported to impart resistance to imatinib, dasatinib and nilotinib therapy.
- a non-limiting example of an ABL1 variant polypeptide contains the polypeptide of SEQ ID NO:3 with one or more of the following modifications: (i) the threonine highlighted in bold text and underlined in the polypeptide of SEQ ID NO:3 herein is substituted to isoleucine, (ii) a polyhistidine tag containing ten consecutive histidine amino acids is appended at the N-terminus along with an adjacent 3’ linker sequence (SSGVDLGT) followed by a “TEV” cleavage site (ENLYFQ/S), and (iii) an initial “MG” sequence.
- SSGVDLGT adjacent 3’ linker sequence
- ENLYFQ/S a “TEV” cleavage site
- An ABL1 variant polypeptide can have the same or about the same substrate phosphorylation activity of an ABL1(wt) polypeptide containing the polypeptide of SEQ ID NO:1 under phosphorylation conditions, when the polypeptide is not contacted by a test compound.
- An ABL1 variant polypeptide can have a substrate phosphorylation activity lower than the phosphorylation activity of an ABL1(wt) polypeptide containing the polypeptide of SEQ ID NO:1 under phosphorylation conditions, when the polypeptide is not contacted by a test compound (for example, a substrate phosphorylation activity within about 10-fold, or 9-fold, or 8-fold, or 7-fold, or 6-fold, or 5-fold, or 4-fold, or 3-fold, or 2-fold, lower than the substrate phosphorylation activity of the ABL1(wt) polypeptide).
- a test compound for example, a substrate phosphorylation activity within about 10-fold, or 9-fold, or 8-fold, or 7-fold, or 6-fold, or 5-fold, or 4-fold, or 3-fold, or 2-fold, lower than the substrate phosphorylation activity of the ABL1(wt) polypeptide.
- An ABL1 variant polypeptide can have a substrate phosphorylation activity greater than the phosphorylation activity of an ABL1(wt) polypeptide containing the polypeptide of SEQ ID NO:1 under phosphorylation conditions, when the polypeptide is not contacted by a test compound (for example, a substrate phosphorylation activity within about 10- fold, or 9-fold, or 8-fold, or 7-fold, or 6-fold, or 5-fold, or 4-fold, or 3-fold, or 2-fold, greater than the substrate phosphorylation activity of the ABL1(wt) polypeptide).
- a test compound for example, a substrate phosphorylation activity within about 10- fold, or 9-fold, or 8-fold, or 7-fold, or 6-fold, or 5-fold, or 4-fold, or 3-fold, or 2-fold, greater than the substrate phosphorylation activity of the ABL1(wt) polypeptide.
- Phosphorylation activity of an ABL1 variant polypeptide can be determined by a suitable assay, which can be an in vitro assay (for example, a labeled peptide cleavage assay described herein), for example.
- a suitable assay for example, a labeled peptide cleavage assay described herein
- Protein kinase inhibitor assessment A compound herein can inhibit a protein kinase (PK) activity.
- PK protein kinase
- a compound can be assessed as a test compound in a suitable assay or system to determine PK inhibitor activity.
- a test compound assessed by an assay for PK inhibitor activity sometimes is a compound herein and/or sometimes is another compound, such as a clinically approved PK inhibitor, for example.
- An assay sometimes is conducted in vitro or in vivo.
- An in vitro assay sometimes quantifies substrate phosphorylation activity catalyzed by a PK polypeptide under phosphorylation conditions in the presence or absence of a test compound that can bind to the PK and potentially inhibit the PK phosphorylation activity.
- a suitable substrate can be utilized in an assay, such as a polypeptide or peptide substrate, for example.
- a peptide substrate for assessing ABL1 inhibitor activity can contain the amino acid sequence EAIYAAPFAKKK (SEQ ID NO:7), for example.
- An assay for quantifying substrate phosphorylation activity inhibition sometimes outputs one or more of an IC50 value, Ki value, Kd value, Koff value and Kon value as a quantification of PK inhibition and/or binding.
- a non-limiting example of an assay for quantifying substrate phosphorylation activity inhibition analyzes a peptide substrate capable of being phosphorylated by a PK polypeptide, referred to herein as an "PK peptide substrate.”
- a PK peptide substrate sometimes is labeled with one or more detectable labels (for example, a fluorescent agent). Fluorescence from a PK peptide substrate labeled with a fluorescent agent sometimes is assessed in an assay.
- a PK peptide substrate end-labelled with a distinct donor fluorophore on one end and a distinct acceptor fluorophore on the other end is utilized.
- the donor and the acceptor fluorophores are a Fluorescence Resonance Energy Transfer (FRET) pair.
- FRET Fluorescence Resonance Energy Transfer
- the donor fluorophore is coumarin and the acceptor fluorophore is fluorescein.
- a PK peptide substrate is cleaved in an assay after the peptide is exposed to phosphorylation conditions.
- a labeled peptide cleavage assay includes: (1) contacting an unphosphorylated peptide, labeled at each end with a FRET pair fluorophore, with a test compound and a PK polypeptide having a PK phosphorylation activity, under phosphorylation conditions, thereby generating a phosphorylated peptide; (2) exposing the peptide, after (1), to phosphorylation state-dependent cleavage conditions, thereby generating cleaved peptide; and (3) measuring and analyzing, after (2) a fluorescent emission signal from one or both fluorophores.
- a PK polypeptide typically is capable of transferring a phosphate from a provided cofactor (for example, adenosine triphosphate (ATP)) to the substrate (for example, peptide or protein substrate), where presence of a PK inhibitor compound reduces the amount of substrate phosphorylation compared to conditions in which the compound is not present.
- a provided cofactor for example, adenosine triphosphate (ATP)
- ATP adenosine triphosphate
- the phosphorylated substrate, but not the unphosphorylated substrate is capable of being cleaved, or (ii) the phosphorylated substrate is preferentially cleaved relative to the unphosphorylated substrate, or (iii) the unphosphorylated substrate, but not the phosphorylated substrate, is capable of being cleaved, or (iv) the unphosphorylated substrate is preferentially cleaved relative to the phosphorylated substrate.
- the substrate typically is exposed to cleavage conditions after the substrate is contacted with a PK polypeptide under phosphorylation conditions.
- the substrate can be cleaved by a peptidase or protease enzyme under cleavage conditions. After the substrate is exposed to phosphorylation conditions and cleavage conditions, a fluorescent signal from cleaved substrate can be measured.
- a ratio of donor emission to acceptor emission (or a ratio of acceptor emission to donor emission) after excitation of the donor can be determined to assess the degree of peptide cleavage and thereby degree of peptide phosphorylation.
- An IC50 value can be determined from such a ratio as known in the art.
- a tracer binding assay measures test compound binding to a PK.
- a PK is contacted with (i) a tracer ligand, labeled with a FRET pair fluorophore, that binds to the PK under binding conditions; (ii) a test molecule that displaces the tracer ligand when the test molecule binds to the PK under the binding conditions; and (iii) an antibody, conjugated to another FRET pair fluorophore, that binds to the PK.
- Binding of the antibody and tracer ligand to the PK results in a FRET signal, and displacement of tracer ligand from the PK by a test molecule that competes with the tracer ligand for binding to the PK results in a reduction of the FRET signal.
- Another type of assay that can be utilized to quantify phosphorylation activity inhibition is an adenosine diphosphate (ADP) formation assay.
- the assay can be used to quantify ATP hydrolysis, including the intrinsic ATPase activity of a PK that transfers a terminal phosphate from ATP to water (and not a peptide substrate), thereby generating ADP from ATP.
- a non-limiting example of an ADP formation assay is described in Kashem et al., J.
- Example 9 Another type of assay that can be utilized to quantify binding of a test compound to a PK is a solid phase inhibitor competition assay.
- the assay can be used to quantify binding of a test compound to a PK tagged with a nucleic acid detection tag in competition with a solid phase-associated PK inhibitor.
- the amount of the PK associated with the solid phase assessed by PCR quantification of the detection tag, determines the level of PK binding to the test compound.
- a non-limiting example of a solid phase inhibitor competition assay is a KINOMEscanTM assay (EuroFins Discovery, described in Fabian et al., Nat.
- a compound can be used in a variety of applications.
- a compound can be used to (i) inhibit one or more PKs in vitro, ex vivo, or in vivo, (ii) inhibit one or more PKs in cells, organs and/or tissues administered a composition containing a compound; and/or (iii) inhibit one or more PKs in a subject administered a composition containing the compound.
- a compound can be utilized in studies, including, for example: (i) studies of PK inhibitors (for example, in vitro assay studies); (ii) pre- clinical in vivo animal studies, including xenograft studies in mice and pharmacokinetic studies in higher animals (for example, rats, dogs and/or monkeys); and (iii) human clinical studies.
- a compound herein can be utilized as a reference compound in a study of other compounds (for example, negative control or positive control), such as in an in vitro assay study, pre-clinical study and/or clinical study, for example.
- a compound herein can be (i) for treatment of a medical condition; (ii) prepared as a composition (for example, pharmaceutical composition) or medicament for treatment of a medical condition; and/or (iii) utilized in a method for treating a medical condition in which a compound is administered to a subject in need thereof in an amount sufficient to treat the medical condition (an effective amount).
- the subject can be human (homo sapiens) and can be an adult or pediatric patient.
- a medical condition sometimes is a PK-associated condition, such as a medical condition associated with a PK aberration and/or dysregulation of a PK (for example, dysregulation of a PK gene).
- a PK aberration can be a PK modification, which, for example, can be a nucleic acid translocation or other modification associated with a PK gene
- a PK modification can be outside of a PK gene coding region and result in dysregulation of the PK gene.
- a PK modification can be an addition, deletion or substitution of one or more amino acids in the PK encoded by a PK gene.
- a PK translocation can be within a PK gene coding region and result in a PK gene truncation and/or translocation of a PK gene or portion thereof to a different chromosome or different location of the same chromosome.
- a PK translocation can result in a fusion of a PK gene or portion thereof with another nucleic acid portion from a different chromosome or different location of the same chromosome.
- a PK aberration can result in an altered PK activity relative to the PK activity when the aberration is not present.
- An altered activity can be (i) altered binding affinity to an inhibitor, (ii) altered binding activity to a native binding partner, and/or (iii) increased phosphorylation activity due to PK overexpression or increased intrinsic activity, for example.
- a PK- associated medical condition can be caused by an aberration of (for example, dysregulation and/or modification of) one or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- a medical condition sometimes is a cell proliferative condition such as a cancer for example, and a compound can be used to treat a cancer condition.
- a compound can be used to treat a cancer condition associated with one or more PK modifications, including modification of one or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- PK modifications including modification of one or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family
- Cancers include leukemia or lymphoid malignancies, hematologic malignancies, such as Hodgkin's lymphoma; non-Hodgkin's lymphomas, including Burkitt's lymphoma, small lymphocytic lymphoma/chronic lymphocytic leukemia, mycosis fungoides, mantle cell lymphoma, follicular lymphoma, diffuse large B-cell lymphoma, marginal zone lymphoma, hairy cell leukemia and lymphoplasmacytic leukemia; tumors of lymphocyte precursor cells, including B-cell acute lymphoblastic leukemia/lymphoma and T-cell acute lymphoblastic leukemia/lymphoma; thymoma; tumors of the mature T and NK cells, including peripheral T-cell leukemias, adult T-cell leukemia/T- cell lymphomas and large granular lymphocytic leukemia; Langerhans cell histocytosis; a my
- Cancers include colorectal and head and neck tumors; squamous cell carcinoma of the head and neck; brain tumors such as glioblastomas; tumors of the lung, breast, pancreas, esophagus, bladder, kidney, ovary, cervix, and prostate; central nervous system neoplasms; neuroblastomas; capillary hemangioblastomas; meningiomas and cerebral metastases; melanoma; gastrointestinal and renal carcinomas and sarcomas; rhabdomyosarcoma; glioblastoma, including glioblastoma multiforme; leiomyosarcoma; lymphoma; blastoma; neuroendocrine tumors; mesothelioma; schwannoma; meningioma; tumors of the central nervous system, including glioma, glioblastoma, neuroblastoma, astrocytoma, medulloblastom
- a cancer can be treated with a composition containing a compound herein as an active ingredient, and in certain embodiments a composition used to treat a cancer contains a compound of Subgroup 1 or Subgroup 5.
- Particular blood cancers include leukemias, and leukemias include chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL).
- CML that can be treated includes chronic phase CML (CML-CP), acute phase CML (CML-AP) and blast phase CML (CML-BP).
- An ALL that can be treated includes a relapsed and/or refractory ALL (R/R ALL), Philadelphia chromosome-positive ALL, and other forms of ALL described herein (for example, Philadelphia chromosome-positive-like- ALL, B-ALL, T-ALL).
- R/R ALL relapsed and/or refractory ALL
- Philadelphia chromosome-positive ALL for example, Philadelphia chromosome-positive-like- ALL, B-ALL, T-ALL.
- a leukemia sometimes is associated with an ABL family PK aberration, and sometimes an ABL1 PK aberration.
- a compound that inhibits an ABL family PK can be used to treat a leukemia (for example, CML and/or an ALL such as Philadelphia chromosome-positive ALL).
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally JAK1, can be used to treat a leukemia (for example, a CML and/or an ALL such as Philadelphia chromosome-positive ALL).
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, AURKA, JAK2 and JAK3, and optionally mildly inhibits or ineffectively inhibits JAK1 can be used to treat a leukemia (for example, a CML and/or an ALL).
- a leukemia can be a Philadelphia chromosome-positive-like ALL, which has been associated with a rearrangement involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, NTRK3, PDGFRB, PTK2B, TSLP and/or TYK2 and/or a sequence mutations involving FLT3, IL7R and/or SH2B3 (see, for example, Roberts et al., N Engl J Med 371(11): 1005-1015 (2014)).
- a compound that effectively inhibits or moderately inhibits ABL2, TYK2, TRKC and PTK2B can be used to treat a Philadelphia chromosome-positive-like ALL.
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally JAK1, can be used to treat a Philadelphia chromosome-positive-like ALL.
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally mildly inhibits or ineffectively inhibits JAK1, can be used to treat a Philadelphia chromosome-positive-like ALL.
- a compound that effectively inhibits or moderately inhibits one or more of all of TYK2, a TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F can be used to treat a Philadelphia chromosome-positive-like ALL.
- a Philadelphia chromosome-positive-like ALL can be treated with a compound of Subgroup 1.
- a leukemia can be a B-cell acute lymphoblastic leukemia (B-ALL).
- a B-ALL can be a TCF3-HLF- positive B-ALL, which can be a TCF3-HLF-positive acute B-ALL.
- a TCF3-HLF-positive B-ALL typically is a B-ALL harboring a t(17;19)(q22;p13) translocation, producing an aberrant TCF3-HLF fusion (see, for example, Leonard et al., Haematologica 106(11): 2990-2994 (2021)).
- a TCF3-HLF- positive B-ALL can be associated with an AURKA aberration, and a compound that effectively inhibits or moderately inhibits an AURKA PK can be used to treat a B-ALL, such as a TCF3-HLF- positive B-ALL for example.
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1- T315I, BTK, AURKA, JAK2 and JAK3, and optionally JAK1, can be used to treat a B-ALL, such as a TCF3-HLF-positive B-ALL for example.
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally mildly inhibits or ineffectively inhibits JAK1, can be used to treat a B-ALL, such as a TCF3-HLF-positive B-ALL for example.
- a compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2, NTRK3 (for example, a ETV6–NTRK3 fusion), PTK2B, TYK2 and ABL2 can be used to treat a B- ALL, such as a TCF3-HLF-positive B-ALL for example, where the compound optionally can effectively inhibit or moderately inhibit JAK1 or the compound optionally can mildly inhibit or ineffectively inhibit JAK1.
- the cancer is associated with an EPHA1 aberration, EPHA2 aberration and/or an EPHB1 aberration, non-limiting examples of which include a breast cancer, lung cancer, brain cancer, spinal cancer, gastric cancer, or skin cancer, and optionally a solid tumor cancer.
- the lung cancer is non-small cell lung cancer (NSCLC); the skin cancer is myeloma; and the brain cancer or spinal cancer is a glioblastoma.
- NSCLC non-small cell lung cancer
- a compound that inhibits a TNK family PK can be utilized to treat a cancer associated with a TNK family PK aberration.
- a cancer is associated with a TNK1 PK aberration, such as a cancer deficient in LKB1, for example.
- a JAK2- associated medical condition is a cancer, including without limitation, a lung cancer, breast cancer, head cancer or neck cancer.
- a JAK2-associated medical condition is a blood cancer, including without limitation, myelodysplastic syndrome (MDS), myelofibrosis, polycythemia vera or essential thrombocythemia.
- MDS myelodysplastic syndrome
- a JAK2-associated cancer is positive for a JAK2 variant containing a V617F substitution.
- a compound that inhibits a RET family PK can be utilized to treat a cancer associated with a RET family PK aberration (for example, a cancer associated with a RET family PK fusion).
- a cancer associated with a RET family PK is lung cancer, including non-small cell lung cancer (NSCLC) and/or lung adenocarcinoma; a thyroid cancer, including medullary thyroid cancer (MTC), thyroid gland medullary carcinoma and/or papillary thyroid cancer (PTC); a colon cancer, including colon adenocarcinoma; and/or a skin cancer including melanoma and/or cutaneous melanoma.
- NSCLC non-small cell lung cancer
- MTC medullary thyroid cancer
- PTC papillary thyroid cancer
- a colon cancer including colon adenocarcinoma
- a skin cancer including melanoma and/or cutaneous melanoma.
- a compound utilized to treat a cancer associated with a RET family PK sometimes is a Subgroup 2 compound.
- a compound that inhibits a PLK4 family PK can be utilized to treat a cancer associated with a PLK family PK aberration.
- a cancer is associated with a PLK4 aberration, non- limiting examples of which include liver cancer, breast cancer and AML.
- a compound utilized to treat a cancer associated with a PLK4 family PK sometimes is a Subgroup 2 compound.
- a compound that inhibits an IRAK family PK can be utilized to treat a cancer associated with an IRAK family PK aberration.
- a cancer is associated with an IRAK3 aberration.
- a compound can be used to treat minimum residual disease (MRD) associated with a cancer condition, and can be a compound that inhibits a JAK family PK.
- MRD minimum residual disease
- a compound that is an effective inhibitor, or optionally a moderate inhibitor, of a JAK PK can be used to treat a cancer condition with potentially higher efficacy, as compared to treatment of the condition with a compound that is not an effective inhibitor or not a moderate inhibitor of a JAK PK.
- a compound that is an effective inhibitor of, or moderate inhibitor of, a JAK family PK, and an effective inhibitor of or moderate inhibitor of one or more other family PKs can be used to treat, with potentially high efficacy, a cancer associated with the one or more other family PKs.
- the autoimmune condition is atopic dermatitis, non-segmental vitiligo or rheumatoid arthritis.
- the rheumatoid arthritis is intolerant to one or more tumor necrosis factor (TNF) blockers.
- TNF tumor necrosis factor
- the skin condition is atopic dermatitis, non-segmental vitiligo, psoriasis (for example, plaque psoriasis), ultraviolet (UV) damaged skin, severely UV damaged skin or aged skin.
- a topical cream containing a compound can be used to treat a inflammation condition, autoimmune condition or skin condition.
- a compound is used to treat a medical condition associated with a TYK family PK aberration, such as a medical condition associated with a TYK2 PK aberration.
- a compound is used to treat psoriasis, which can be moderate to severe psoriasis.
- a compound is used to treat plaque psoriasis, which can be moderate to severe plaque psoriasis.
- a compound is used to treat a subject who is a candidate for systemic therapy or phototherapy.
- the compound inhibits a TYK family PK, and in certain instances, the compound inhibits TYK2(wt).
- the compound is a Subgroup 3 compound.
- a compound that is an effective inhibitor and selective inhibitor of a JAK2 PK can be used to treat a condition with a potentially lower incidence of a serious adverse event, as compared to treatment of the condition with a compound that is not a selective inhibitor of a JAK2 PK.
- Non-limiting examples of compounds that are not selective inhibitors of JAK2 PK are tofacitinib or ruxolitinib.
- a serious adverse event can be a malignancy, serious adverse cardiovascular event and/or blood clot, mortality or infection.
- a compound that is an effective inhibitor and selective inhibitor of a JAK2 PK can be utilized to treat a condition in a subject having a prior history of heart disease, and to whom a compound that is not a selective inhibitor of JAK2 would not be administered.
- a moderate to severe form of a medical condition can be treated.
- moderate to severe rheumatoid arthritis or moderate to severe plaque psoriasis can be treated.
- a stage III or stage IV cancer condition can be treated (for example, a stage IV ROS1 positive lung cancer), for example.
- a medical condition associated with a particular variant PK can be treated.
- a blood cancer such as myelofibrosis, MDS, polycythemia vera or essential thrombocytopenia, for example, can be treated in subjects from which a sample was assessed as having a JAK2 containing a V617F variation.
- Such subjects can be treated with a compound that effectively inhibits a JAK2 variant containing the V617F.
- a leukemia such as CML or Philadelphia chromosome-positive ALL, for example, can be treated in subjects from which a sample was assessed as having an ABL1 variant containing a T315I substitution.
- presence or absence of a DDR2 variant containing N456S and/or T654M substitution is screened in a sample from a subject, and if the variant is present in the sample, the subject may be treated for a particular medical condition associated with the variant (for example, a lung cancer such as non-small cell lung cancer (NSCLC)).
- a lung cancer such as non-small cell lung cancer (NSCLC)
- a RET variant containing one or more of A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F is screened in a sample from a subject, and if the variant is present in the sample, the subject may be treated for a particular medical condition associated with the variant (for example, a lung cancer (NSCLC) or thyroid cancer (medullary thyroid cancer (MTC), papillary thyroid cancer (PTC) or thyroid gland medullary carcinoma, for example)).
- NSCLC lung cancer
- MTC medullary thyroid cancer
- PTC papillary thyroid cancer
- TGF thyroid gland medullary carcinoma
- Non- limiting examples of desired results include reducing a PK activity (e.g., test compound binding activity; substrate phosphorylation activity); decreasing, attenuating and/or stabilizing one or more symptoms associated with a condition; increasing quality of life of a subject suffering from a condition; decreasing the dose of other medications required to treat the condition; enhancing the effect of another medication; delaying the progression of the condition; and/or prolonging survival of a subject.
- PK activity e.g., test compound binding activity; substrate phosphorylation activity
- symptoms associated with cancer include presence and/or proliferation of cancer cells; presence and/or growth of one or more tumors; cancer metastases and the like.
- An effective amount can be an amount sufficient to: kill cancer cells; reduce the rate of cancer cell proliferation; and/or eliminate, reduce and/or delay metastasis from a primary site of cancer.
- An effective amount may be in conjunction with another therapeutic agent.
- An effective amount may be considered in the context of administering a compound described herein without another therapeutic agent or with another therapeutic agent.
- An optimal range of an effective amount of each component can be determined.
- An effective amount can be determined by standard clinical techniques and can be a technique for determining dosage.
- An effective amount often depends on the route of administration and the seriousness of the condition, and often is decided according to the judgment of the practitioner and circumstances of each subject.
- An effective amount can be administered in one or more administrations.
- Non-limiting types of administration include parenteral administration (e.g., intradermal, intramuscular, intraperitoneal, intravenous and subcutaneous), epidural, and mucosal (e.g., intranasal and oral routes).
- Administration may be by any suitable route, for example, by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, and the like), and may be by pulmonary administration (e.g., use of an inhaler or nebulizer, and formulation with an aerosolizing agent).
- An effective amount may be delivered by liposomes, microparticles and/or microcapsules in certain implementations.
- An effective dosage of an active ingredient can be determined by assessing its in vitro activity in a cell or tissue system and/or in vivo activity in an animal system. For example, methods for extrapolating an effective dosage in mice and other animals to humans are known (see, for example, U.S.
- Such systems can be used for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population) of an active ingredient.
- the dose ratio between a toxic and therapeutic effect is the therapeutic index and it can be expressed as the ratio ED50/LD50.
- a dosage of an active ingredient often lies within a range of circulating concentrations for which the ED50 is associated with low toxicity or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
- a therapeutically effective dose of an active ingredient can be estimated initially from cell culture assays.
- Such “imprinted” affinity matrixes are amenable to ligand-binding assays, whereby the immobilized monoclonal antibody component is replaced by an appropriately imprinted matrix (see, for example, Vlatakis, et al., Nature (1993) 361:645-647).
- isotope-labeling By the use of isotope-labeling, "free" concentration of an active ingredient can be readily monitored and used in calculations of IC50.
- Such “imprinted” affinity matrixes can also be designed to include fluorescent groups having photon-emitting properties that measurably change upon local and selective binding of an active ingredient. These changes can be readily assayed in real time using appropriate fiberoptic devices, in turn allowing the dose in a test subject to be quickly optimized based on its individual IC50.
- Non-limiting examples of doses include milligram or microgram amounts of an active ingredient per kilogram of subject or sample weight, for example, about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about 1 microgram per kilogram to about 50 micrograms per kilogram. It is understood that appropriate doses of a small molecule depend upon the potency of the small molecule with respect to the expression or activity to be modulated.
- a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained.
- the specific dose level for any particular animal subject will depend upon a variety of factors including the activity of the specific active ingredient employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.
- A10 The composition of any one of embodiments A1-A7, wherein R 3 is methyl or methoxy and R 1 and R 2 each is hydrogen.
- A11 The composition of any one of embodiments A1-A7 and A10, wherein R 3 is methyl and R 1 and R 2 each is hydrogen.
- composition of embodiment A1 where R 1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R 2 , R 3 and R 5 each is hydrogen; and R 4 and R 6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo, with the proviso that R 4 or R 6 , or R 4 and R 6 , is not hydrogen.
- R 1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy
- R 4 and R 6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo, with the proviso that R 4 or R 6 , or R 4 and R 6 , is not hydrogen.
- A13 The composition of embodiment A12, where R 1 is an unsubstituted C1-C4 alkyl, ethyl or methyl
- composition of embodiment A12 of A13 where (i) R 4 is unsubstituted C1-C4 alkoxy or isopropyloxy; (ii) R 6 is fluoro or chloro; or a combination of (i) and (ii). A15.
- composition of embodiment A1 where R 3 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R 1 , R 2 , R 4 , R 5 and R 6 each is hydrogen.
- A20 The composition of embodiment A19, where R 3 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
- A21 The composition of embodiment A19 or A20, where the compound is 4-((4-methyl-3-((8- phenylquinazolin-2-yl)amino)phenyl)carbamoyl)benzoic acid (compound C13) or a pharmaceutically acceptable salt thereof.
- C1.4. The composition of any one of embodiments A1-A21, B1-B6 and C1, with the proviso that R 6 is not methoxy.
- a composition comprising 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- a composition comprising 4-((5-((8-(2-isopropylphenyl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- a composition comprising 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- a composition comprising 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- a composition comprising 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- a composition comprising 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- a composition comprising 4-((4-methyl-3-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
- D5. The composition of any one of embodiments D1-D4, wherein R 1 , R 2 and R 3 each is hydrogen.
- D6. The composition of any one of embodiments D1-D5, wherein R 10 , R 11 , R 12 and R 13 each independently is hydrogen or methoxy.
- D7 The composition of any one of embodiments D1-D6, wherein R 10 and R 12 each is hydrogen.
- D8. The composition of any one of embodiments D1-D7, wherein R 11 and R 13 each is methoxy. D9.
- composition of any one of embodiments D1-D16, with the proviso that R 11 and/or R 12 is not O H N O H H 3 C H N O H3C N O O H C N N N N H 3 C S S 3 S or - CH2C(OH)(CH3)CH3, or -CH2CH2F. D21.
- the composition of any one of embodiments D1-D16, with the proviso that R 10 , R 11 , R 12 or R 13 is not . of any one of embodiments D1-D16, with the proviso that R 10 , R 11 , R 12 or R 13 is not (i) one of the following designated Group A electrophilic groups: ; or (ii) one of the following designated Group B electrophilic groups:
- D29. The composition of any one of embodiments D1-D16, with the proviso that R 14 and the N to which it is covalently attached do not together form a heterocycloalkyl or substituted heterocycloalkyl.
- composition of any one of embodiments D1-D16, with the proviso that R 14 and the N to which it is covalently attached do not together contain a heterocycloalkyl or substituted heterocycloalkyl.
- D31. The composition of any one of embodiments D1-D16, with the proviso that R 14 is not a heterocycloalkyl or substituted heterocycloalkyl.
- D32. The composition of any one of embodiments D1-D16, with the proviso that R 14 does not contain a heterocycloalkyl or substituted heterocycloalkyl.
- E1. The composition of any one of embodiments A1-A21, B1-B6, C1-C12 and D1-D32 which is a pharmaceutical composition.
- composition of embodiment E1 where the compound is capable of inhibiting an activity of a protein kinase (PK).
- PK protein kinase
- E3. The composition of embodiment E2, where the PK activity is a PK binding activity and/or a PK catalytic activity.
- E4. The composition of embodiment E2 or E3, where the compound is capable of inhibiting an activity of two or more PKs.
- E5. The composition of any one of embodiments E2-E4 where the compound is capable of effectively inhibiting, moderately inhibiting and/or selectively inhibiting a PK activity.
- E6 The composition of any one of embodiments E1-E5, which is a pharmaceutical composition comprising one or more pharmaceutically acceptable excipients.
- E7. The composition of embodiment E6, for topical administration, oral administration or administration by injection or infusion. F1.
- compositions comprising a compound, the compound comprising a quinazolinyl group and an amine-linked phenyl group for inhibiting two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and a PTK family PK.
- F4 Use of a composition comprising a compound comprising a quinazolinyl group and an amine- linked phenyl group for selectively inhibiting a JAK2 PK.
- F5. The use of embodiment F4, for effectively inhibiting JAK2(wt) PK and not effectively inhibiting JAK1(wt) PK.
- F6. The use of embodiment F4 or F5, for inhibiting a JAK3(wt) PK, optionally for effectively inhibiting a JAK3(wt) PK, and optionally for moderately inhibiting a JAK3(wt) PK.
- F7 Use of a composition comprising a compound comprising a quinazolinyl group and an amine- linked phenyl group for selectively inhibiting a JAK2 PK.
- any one of embodiments F1-F8 for effectively inhibiting two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- embodiment F9 or F10 for not effectively inhibiting and/or for not moderately inhibiting one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK.
- any one of embodiments F1-F11 for inhibiting an ABL family PK, optionally inhibiting ABL1(wt), optionally inhibiting one or more ABL1 variants, optionally inhibiting ABL2(wt), and/or optionally inhibiting one or more ABL2 variants; where the one or more ABL1 variants optionally comprise one or more of the following amino acid substitutions relative to ABL1(wt): T315I, G250E, Q252H, Y253F, E255K, F317L, M351T and H396P.
- F13 The use of any one of embodiments F1-F12, for effectively inhibiting ABL1, ABL1-T315I, AURKA, and JAK2.
- F14 The use of embodiment F13, for effectively inhibiting or moderately inhibiting BTK.
- F15 The use of embodiment F13 or F14, for effectively inhibiting or moderately inhibiting JAK3.
- F16 The use of any one of embodiments F13-F15, for effectively inhibiting or moderately inhibiting JAK1.
- F17 The use of any one of embodiments F13-F16, for mildly inhibiting or ineffectively inhibiting JAK1.
- F18 The use of any one of embodiments F13-F17, for effectively inhibiting or moderately inhibiting one or more or all of TYK2, A TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F. F19.
- any one of embodiments F13-F18 for effectively inhibiting or moderately inhibiting one or more or all of TRKA, TRKB, TRKC, ROS1, EPHA1 and EPHB1.
- F20 The use of any one of embodiments F13-F19, for effectively inhibiting or moderately inhibiting a SRC family PK and/or a DDR family PK.
- F21 The use of any one of embodiments F13-F20, for effectively inhibiting or moderately inhibiting ABL2.
- F22 The use of any one of embodiments F13-F21, for effectively inhibiting or moderately inhibiting PTK2B.
- F23 The use of any one of embodiments F13-F18, for effectively inhibiting or moderately inhibiting one or more or all of TRKA, TRKB, TRKC, ROS1, EPHA1 and EPHB1.
- F20 The use of any one of embodiments F13-F19, for effectively inhibiting or moderately inhibiting a SRC family PK and/or a DDR family PK.
- F21 The use
- F26 The use of embodiment F25, for inhibiting, optionally effectively inhibiting or optionally moderately inhibiting TYK2(wt). F27.
- any one of embodiments F1-F22, F25 and F26 for inhibiting a RET family PK, and optionally: inhibiting RET(wt) and/or one or more RET variants, where the one or more RET variants optionally comprise one or more of the following amino acid substitutions relative to RET(wt): A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F.
- F28 The use of any one of embodiments F25-F27, where the composition comprises a compound of any one of embodiments A16-A18. F29.
- any one of embodiments F1-F22 and F25-F27 for inhibiting a PLK family PK, and optionally: inhibiting PLK4(wt) and/or one or more PLK4 variants.
- F30 The use of embodiment F29, where the composition comprises a compound of any one of embodiments A19-A21.
- F31 The use of any one of embodiments F1-F30, for inhibiting a PK activity, optionally for inhibiting a PK binding activity, and/or optionally for inhibiting a PK phosphorylation activity.
- F32 The use of any one of embodiments F1-F30, where the PK is a homo sapiens PK. F33.
- any one of embodiments F1-F31 which is in vitro or ex vivo.
- F34 The use of any one of embodiments F1-F31, which is in vivo.
- F35 The use of embodiment F33 or F34, which is in cells, an organ and/or a tissue.
- F36 The use of embodiment F34 or F35, which is in a subject.
- G1. Use of a compound or composition of any one of embodiments A1-A21, B1-B6, C1-C12, D1- D32 and E1-E7, for treatment of a medical condition or for preparation of a medicament for treatment of a medical condition.
- any one of embodiments F1-F36 for treatment of a medical condition or for preparation of a medicament for treatment of a medical condition.
- G3. The use of embodiment G1 or G2, where the medical condition is associated with a protein kinase (PK) aberration.
- PK protein kinase
- G4. The use of embodiment G3, where the medical condition is associated with dysregulation of a PK and/or is associated with a PK modification.
- PK is one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, SRC family PK, DDR family PK, and/or PTK family PK.
- G6 The use of any one of embodiments G1-G5, where the medical condition is a cancer.
- G7. The use of embodiment G6, where the cancer is a lymphoma, thymoma, leukemia, carcinoma, glioma, sarcoma, liposarcoma, adenocarcinoma, adenosarcoma or adenoma.
- embodiment G6 where the cancer is a cancer occurring in one or more of blood, lymph node, thymus, thyroid, breast, heart, lung, small intestine, colon, rectum, spleen, kidney, bladder, head, neck, esophagus, ovary, prostate, brain, pancreas, skin, bone, bone marrow, uterus, testicles, cervix and liver.
- embodiment G8 where the cancer is a blood cancer.
- embodiment G10 where the blood cancer is a leukemia, myelodysplastic syndrome (MDS), myelofibrosis, polycythemia vera or essential thrombocythemia.
- MDS myelodysplastic syndrome
- embodiment G10 where the leukemia is acute myeloid leukemia (AML), chronic myeloid leukemia (CML) or acute lymphoblastic leukemia (ALL).
- AML acute myeloid leukemia
- CML chronic myeloid leukemia
- ALL acute lymphoblastic leukemia
- embodiment G11 where the CML is chronic phase CML (CML-CP), acute phase CML (CML-AP) and blast phase CML (CML-BP).
- CML-CP chronic phase CML
- CML-AP acute phase CML
- CML-BP blast phase CML
- embodiment G11 where the ALL is a relapsed and/or refractory ALL (R/R ALL).
- embodiment G11 or G13 where the ALL is Philadelphia chromosome-positive ALL, Philadelphia chromosome-positive-like-ALL, B-cell acute lymphoblastic leukemia (B-ALL) or T-cell acute lymphoblastic leukemia (T-ALL).
- B-ALL B-cell acute lymphoblastic leukemia
- T-ALL T-cell acute lymphoblastic leukemia
- G15 The use of any one of embodiments G11, where the cancer is ALL and optionally the ALL is Philadelphia chromosome-positive ALL.
- embodiment G14 where the ALL is Philadelphia chromosome-positive-like ALL.
- G17 The use of any one of embodiments G15 or G16, where the cancer is associated with an ABL family PK aberration and optionally an ABL1 family PK aberration.
- embodiment G17 where the compound effectively inhibits or moderately inhibits ABL1 and optionally ABL1-T315I.
- G19. The use of embodiment 14, where the cancer is a B-ALL, optionally is a TCF3-HLF-positive B-ALL, or optionally is a TCF3-HLF-positive acute B-ALL.
- G20. The use of embodiment G19, where the cancer is associated with an AURK family PK aberration.
- embodiment G21 The use of embodiment G19 or G20, where the compound effectively inhibits or moderately inhibits an AURKA family PK; and/or (ii) effectively inhibits or moderately inhibits an ABL1 family PK, optionally ABL1, and optionally ABL1-T315I.
- G23. The use of embodiment G22, where the lung cancer is NSCLC.
- G24. The use of embodiment G22 or G23, where the lung cancer is associated with a DDR family PK aberration and/or a SRC family PK aberration.
- G25. The use of embodiment G24, where the DDR family PK is a DDR2(wt) PK or DDR2 variant PK, and optionally the DDR2 variant PK optionally contains a N456S and/or T654M amino acid substitution.
- any one of embodiments G22-G25 where the compound (i) effectively inhibits or moderately inhibits SRC(wt), SCR-N1(wt), DDR2(wt) and/or a DDR2 variant containing a T654M and/or N456S amino acid substitution.
- G27 The use of any one of embodiments G1-G26, where the medical condition is treated in a subject identified as having an ABL1-T315I variant.
- any one of embodiments G1-G27 where the medical condition is treated in a subject not identified as having an ABL1-T315I variant or identified as not having an ABL1-T315I variant, and is resistant and/or intolerant to at least two PK inhibitors.
- G29 The use of any one of embodiments G1-G28, where the compound effectively inhibits ABL1, ABL1-T315I, AURKA, and JAK2.
- G30 The use of any one of embodiments G1-G29, where the compound effectively inhibits or moderately inhibits BTK.
- G31 The use of any one of embodiments G1-G30, where the compound effectively inhibits or moderately inhibits JAK3.
- G32 The use of any one of embodiments G1-G27, where the medical condition is treated in a subject not identified as having an ABL1-T315I variant or identified as not having an ABL1-T315I variant, and is resistant and/or intolerant to at least two PK inhibitors.
- any one of embodiments G1-G31 where the compound effectively inhibits or moderately inhibits JAK1.
- G33 The use of any one of embodiments G1-G31, where the compound mildly inhibits or ineffectively inhibits JAK1.
- G34 The use of any one of embodiments G1-G33, where the compound effectively inhibits or moderately inhibits one or more or all of TYK2, A TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F. G35.
- any one of embodiments G1-G34 where the compound effectively inhibits or moderately inhibits one or more or all of TRKA, TRKB, TRKC, ROS1, EPHA1 and EPHB1.
- G36 The use of any one of embodiments G1-G35, where the compound effectively inhibits or moderately inhibits a SRC family PK and/or a DDR family PK.
- G37 The use of any one of embodiments G1-G36, where the compound effectively inhibits or moderately inhibits ABL2.
- G38 The use of any one of embodiments G1-G37, where the compound effectively inhibits or moderately inhibits PTK2B.
- any one of embodiments G1-G38 where the a compound of any one of embodiments A1-A21 or optionally A12-A15.
- G40 The use of any one of embodiments G1-G8, where the cancer is a lung cancer, a thyroid cancer, a colon cancer or a skin cancer.
- embodiment G40 where: the lung cancer is a lung nodule cancer, non-small cell lung cancer (NSCLC), small cell lung cancer, lung adenocarcinoma or mesothelioma; the thyroid cancer is medullary thyroid cancer (MTC), papillary thyroid cancer (PTC) or thyroid gland medullary carcinoma; the colon cancer is colon adenocarcinoma; and/or the skin cancer is melanoma or cutaneous melanoma.
- NSCLC non-small cell lung cancer
- MTC medullary thyroid cancer
- PTC papillary thyroid cancer
- the skin cancer is melanoma or cutaneous melanoma.
- G42 The use of embodiment G40 or G41, where the cancer is associated with a RET family PK aberration.
- G43 The use of any one of embodiments G40-G42, where the compound effectively inhibits or moderately inhibits a RET family PK.
- G45. The use of any one of embodiments G1-G8, where the cancer is a liver cancer, breast cancer or AML.
- G46. The use of embodiment G45, where the cancer is associated with a PLK family PK aberration and optionally of a PLK4 family PK aberration.
- G47 The use of embodiments G45 or G46, where the compound effectively inhibits or moderately inhibits a PLK family PK, and optionally the compound is of any one of embodiments A1-A21 or optionally A19-A21.
- any one of embodiments G1-G47, where the medical condition is minimum residual disease (MRD).
- G49. The use of any one of embodiments G1-G5, where the medical condition is an inflammation condition, autoimmune condition and/or skin condition.
- G50. The use of embodiment G49, where: the inflammation condition is a chronic inflammation condition, senescent cell chronic inflammation condition or senescence-associated secretory phenotype condition; the autoimmune condition is atopic dermatitis, non-segmental vitiligo or rheumatoid arthritis; or the skin condition is atopic dermatitis, non-segmental vitiligo, psoriasis, plaque psoriasis, ultraviolet (UV) damaged skin, severely UV damaged skin, aged skin or severely aged skin.
- UV ultraviolet
- G51 The use of embodiment G49 or G50, where the skin condition is atopic dermatitis or non- segmental vitiligo.
- G52 The use of embodiment G49 or G50, where the medical condition is a psoriasis, optionally a moderate to severe psoriasis, optionally a moderate to severe plaque psoriasis, and/or optionally is treated in a subject who is a candidate for systemic therapy or phototherapy.
- G53 The use of any one of embodiments G49-G52, where the medical condition is associated with a TYK family PK aberration and optionally is associated with a TYK2 PK aberration.
- G54 The use of any one of embodiments G49-G52, where the medical condition is associated with a TYK family PK aberration and optionally is associated with a TYK2 PK aberration.
- embodiment G53 where the compound effectively inhibits or moderately inhibits TYK2.
- embodiment G54 where the compound is of any one of embodiments A1-A21 or optionally A16-A18. Examples The examples below illustrate certain implementations and do not limit the technology.
- Example 1 Preparation of ethyl 4-[[5-[(8-bromoquinazolin-2-yl)amino]-2-methyl- phenyl]carbamoyl]benzoate Described in this Example is a process for preparing ethyl 4-[[5-[(8-bromoquinazolin-2-yl)amino]-2- methyl-phenyl]carbamoyl]benzoate, an intermediate for preparing compound C1 in Table A, for example.
- the vial was charged with EEDQ (1.80 g, 7.29 mmol) with rinsing using DMF (5 mL). The vial was sealed and stirred at room temperature (rt) for 24 hours (hr). LCMS showed the reaction was complete. The reaction was poured into excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), then water (1x), then 1N HCl (3x), and finally water. The organic phase was dried over MgSO 4 , filtered and evaporated to a pale yellow foam (1.192 grams). Attempted redissolution of the foam in EtOAc gives a white suspension of apparent solid. However, no filtration was carried out. The product was used without further purification.
- the solution was evaporated to an orange- brown oil. IPA (10 mL) was added and the mixture heated until the residue dissolved. The dark solution was allowed to cool and stir at rt for 2 hr. The dark brown precipitated solid was recovered by filtration. The dark solid in the funnel was dissolved in excess DCM and filtered into a separate rb flask. The black solid remaining in the reaction vials was layered with excess DCM and stirred at rt for an hour, giving an orange-green supernatant. The operation was repeated three more times with the supernatants being collectively recovered. This third mixture was filtered, leaving behind a green solid in the funnel. There were four isolated materials.
- the vial was charged with EEDQ (507 mg, 2.05 mmol) with rinsing using DMF (1.5 mL). The vial was sealed and stirred at rt for 24 hr. LCMS shows the reaction is complete. The reaction was poured into excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), then water (1x), then 1N HCl (3x), and finally water. The organic layer was dried over MgSO4, filtered, and evaporated to a brown oil (169.5 mg). The material was used without further purification.
- EtOH (3 mL each) was added, and the combined solids were agitated using a pipette before sealing.
- the mixtures were heated to 130°C in an aluminum block, and vigorously stirred for 5 hours.
- the two vials were rinsed with excess EtOH, then excess DCM, into a 250 mL round-bottomed flask.
- the solution was evaporated to an orange-brown oil.
- IPA (10 mL) was added, and the mixture heated until the residue dissolved.
- the dark solution was allowed to cool and stir at room temperature for 12 hr.
- the dark brown precipitated solid was recovered by filtration (83.1 mg). The material was used without further purification.
- Example 4 Preparation of C3 Described in this Example is a process for preparing compound C3 shown in Table A.
- Preparation of ethyl 4-((5-((tert-butoxycarbonyl)amino)-2-methoxyphenyl)carbamoyl)benzoate was mg, .
- DMF 2.8 mL
- the vial was next charged with tert-butyl N-(3-amino-4-methoxy-phenyl)carbamate (500 mg, 2.10 mmol) with rinsing using DMF (2.8 mL).
- TEA (524 mL, 3.78 mmol) was added.
- the vial was charged with EEDQ (934 mg, 3.78 mmol) with rinsing using DMF (2.8 mL). The vial was sealed and stirred at rt for 24 hr. LCMS showed the reaction was complete. The reaction was poured into excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), then water (1x), then 1N HCl (3x), and finally water. The organic layer was dried over MgSO 4 , filtered, and evaporated to a yellow oil (304 mg). The material was used without further purification.
- EtOH (2.5 mL each) was added, and the combined solids were agitated using a pipette before sealing.
- the mixtures were placed in a 130°C aluminum block and vigorously stirred for 5 hours.
- the two vials were rinsed with excess EtOH, then excess DCM, into a 250 mL round-bottomed (rb) flask.
- the solution was evaporated to an orange-brown oil.
- IPA (10 mL) was added and the mixture heated until the residue dissolved.
- the dark solution was allowed to cool and stir at room temperature for 12 hr.
- the dark brown precipitated solid was recovered by filtration (126 mg). The material was used without further purification.
- Example 5 Preparation of C4 Described in this Example is a process for preparing compound C4 shown in Table A.
- Aqueous K 3 PO 4 (190 ⁇ L, 2.0 M, 0.38 mmol) was added, followed by tetrakis(triphenylphoshine) palladium (29 mg, 0.025 mmol).
- the vessel was sealed and the mixture heated in an aluminum block (105°C) for 5 hours.
- LCMS indicated the reaction was complete with the formation of the desired product.
- the reaction was diluted with excess iPrOAc.
- MgSO 4 was added and the mixture filtered and evaporated to a brown oil (121 mg). The oil was chromatographed by preparative TLC using 40:1 DCM/MeOH. The major UV active band was isolated (42 mg). The product was used without further purification.
- Example 6 Preparation of C5 Described in this Example is a process for preparing compound C5 shown in Table A.
- Tetrakis(triphenylphosphine)palladium (17.7 mg, 0.015 mmol) was added, the vial sealed, then heated in an aluminum block (105°C) for 5 hours. LCMS indicated the reaction went to completion. The reaction was diluted with excess iPrOAc. MgSO 4 was added, the mixture was filtered, and evaporated to a yellow oil. The oil was purified by preparative thin layer chromatography on two 500 mm pTLC plates using 40:1 DCM:MeOH. The major UV-active band was isolated (yellow solid, 9.1 mg).
- Example 7 Preparation of C6 Described in this Example is a process for preparing compound C6 shown in Table A.
- Example 8 Preparation of C7 Described in this Example is a process for preparing compound C7 shown in Table A.
- Example 9 Protein Kinase Inhibition Assays and Results This Example describes a cell-free assay utilized to identify candidate compounds that bind to and inhibit protein kinase (PK) and PK variants.
- PK protein kinase
- One assay is referred to as a "Z ⁇ -LYTE assay” and is an example of a labeled peptide cleavage assay.
- the fluorescence-based assay relies on the differential sensitivity of a small, dual-end-labelled peptide to cleavage by a protease, dependent on the phosphorylation state of the peptide (FIG.1).
- the peptide substrate is end-labelled with two distinct fluorophores that comprise a Fluorescence Resonance Energy Transfer (FRET) pair.
- FRET Fluorescence Resonance Energy Transfer
- the kinase transfers the gamma-phosphate from ATP to the single, unique tyrosine, serine or threonine in the synthetic FRET peptide.
- the reaction conditions are titrated such that 10-40% of the peptide substrate is phosphorylated.
- a site-specific protease that only recognizes and cleaves the non-phosphorylated FRET peptide is added. Cleavage interferes with FRET between the donor (i.e., coumarin) and the acceptor (i.e., fluorescein) fluorophores on the FRET-peptide substrate, unlike the phosphorylated, uncleaved peptide.
- ER Coumarin Emission (445 nm)/Fluorescein Emission (520 nm).
- ER Coumarin Emission (445 nm)/Fluorescein Emission (520 nm).
- the ER is relatively low, but if kinase-mediated phosphorylation is inhibited, the ER is relatively high.
- This ratiometric approach to quantitating reaction progress virtually eliminates well-to-well variations in FRET-peptide concentration and signal intensities, leading to very high Z’-factor values (> 0.7; World Wide Web URL en.wikipedia.org/wiki/Z-factor) at a low percent phosphorylation.
- Assay regents and conditions are described for an ABL1 PK assay, and are described thereafter for other PK assays.
- Test compounds The Test Compounds are screened in 1% DMSO (final) in the well. For 10-point titrations, 3-fold serial dilutions are conducted from a relatively high starting concentration (e.g., 10 micromolar ( ⁇ M)), considered to be much greater than an IC50 of likely pharmaceutical value.
- ABL1 PK assay reagents All Peptide/Kinase Mixtures are diluted to a 2X working concentration in the appropriate Kinase Buffer.
- the 2X ABL1 polypeptide/ Tyr 02 substrate peptide mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 0.3 - 1.2 ng ABL1 (or 1.36 – 6 ng ABL1(T315I)) and 2 ⁇ M Tyr 02 in 50 mM HEPES, pH 7.5, 0.01% BRIJ- 35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent A is added.
- the ABL1(wt) polypeptide utilized for the assay described in this Example was the "isoahABL1(wt)" polypeptide described herein (SEQ ID NO:4), which is referred to as “ABL1” in Table 1 and "ABL1(wt)” or “WT” in Table 3 of this Example.
- the ABL1 variant polypeptides utilized contained the same polypeptide as the "isoahABL1(wt)" polypeptide except that each contained one corresponding amino acid substitution chosen from E255K, F317I, F317L, G250E, T315I or Y253F.
- ABL1 variant polypeptides are referred to as "ABL1 E255K,” “ABL1 F317I,” “ABL1 F317L,” “ABL1 G250E,” “ABL1 T315I” and “ABL1 Y253F” in Table 1 of this Example according to the corresponding amino acid substitution contained and are referred to in Table 3 of this Example according to the corresponding amino acid substitution contained.
- All ATP Solutions are diluted to a 4X working concentration in Kinase Buffer (50 mM HEPES, pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA).
- the ATP Km apparent (Km app) is previously determined using a Z ⁇ -LYTE assay.
- Table 1 in this Example shows IC 50 values for particular inhibitors of phosphorylation activity for ABL1(wt) polypeptide and ABL1 variant polypeptides.
- Table 1 The Development Reagent (i.e., with protease) is diluted in Development Buffer. Assay Protocol Bar-coded Corning, low volume NBS, black 384-well plate (Corning Cat.
- 0% Phosphorylation Control (100% Inhibition Control) The maximum Emission Ratio is established by the 0% Phosphorylation Control (100% Inhibition Control), which contains no ATP and therefore exhibits no kinase activity. This control yields 100% cleaved peptide in the Development Reaction. 100% Phosphorylation Control The 100% Phosphorylation Control, which contains a synthetically phosphorylated peptide of the same sequence as the peptide substrate, is designed to allow for the calculation of percent phosphorylation. This control yields a very low percentage of cleaved peptide in the Development Reaction. The 0% Phosphorylation and 100% Phosphorylation Controls allow one to calculate the percent Phosphorylation achieved in a specific reaction well.
- Control wells do not include any kinase inhibitors.
- 0% Inhibition Control The minimum Emission Ratio in a screen is established by the 0% Inhibition Control, which contains active kinase. This control is designed to produce a 10–50% phosphorylated peptide in the Kinase Reaction. Cascade assays may produce up to 70% phosphorylated peptide.
- Known Inhibitor A known inhibitor control standard curve, 10-point titration, is run for each individual kinase on the same plate as the kinase to ensure the kinase is inhibited within an expected IC50 range previously determined.
- the following controls are prepared for each concentration of Test Compound assayed: Development Reaction Interference
- the Development Reaction Interference is established by comparing the Test Compound Control wells that do not contain ATP versus the 0% Phosphorylation Control (which does not contain the Test Compound).
- the expected value for a non-interfering compound should be 100%. Any value outside of 90% to 110% is flagged.
- Test Compound Fluorescence Interference The Test Compound Fluorescence Interference is determined by comparing the Test Compound Control wells that do not contain the Kinase/Peptide Mixture (zero peptide control) versus the 0% Inhibition Control.
- the expected value for a non-fluorescence compound should be 0%. Any value > 20% is flagged.
- Graphing Software SelectScreen Kinase Profiling Service uses XLfit from IDBS.
- the dose response curve is curve fit to model number 205 (sigmoidal dose-response model). If the bottom of the curve does not fit between -20% & 20% inhibition, it is set to 0% inhibition. If the top of the curve does not fit between 70% and 130% inhibition, it is set to 100% inhibition.
- Z′-LYTE Data Analysis The equations shown in the following Table 2 of this Example are used for each set of data points: Table 2 The description of the assay in this Example is excerpted from (Z’LYTETM Screening Protocol and Assay Conditions (rev 29 Jan 2021)).
- AURKA Aurora A
- AURKB Aurora B
- the 2X AURKA (Aurora A) / Ser/Thr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 0.75 - 3 ng AURKA (Aurora A) or 3.5 - 18 ng AURKB (Aurora B) and 2 ⁇ M Ser/Thr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- 5 ⁇ L of a 1:4096 dilution of Development Reagent A is added.
- AURKC (Aurora C): The 2X AURKC (Aurora C) / Ser/Thr 19 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 ⁇ L Kinase Reaction contains 2 - 20 ng AURKC (Aurora C) and 2 ⁇ M Ser/Thr 19 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 ⁇ L of a 1:256 dilution of Development Reagent A is added.
- BTK, BMX and ITK The 2X BTK / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 0.52 - 3.36 ng BTK, or 2.5 - 10 ng BMX, or 4.69 - 60 ng ITK, and 2 ⁇ M Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- 5 ⁇ L of a 1:128 dilution of Development Reagent B is added.
- JAK1, JAK2 and JAK3 The 2X JAK1 / Tyr 06 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3.
- the final 10 ⁇ L Kinase Reaction contains 22.9 - 91.5 ng JAK1, or 0.12 - 0.5 ng JAK2, 1.75 – 9 ng JAK2 JH1-JH2-V617F, or 0.5 - 2.7 ng JAK3 and 2 ⁇ M Tyr 06 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3.
- EPHA1 and EPHB1 The 2X EPHA1 / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 ⁇ L Kinase.
- the reaction contains 3.12 - 38.6 ng EPHA1 (or 1.2 – 4.8 ng EPHA8, or 2.4 – 10 ng EPHB1, or 0.55 – 2.86 ng EPHB1) and 2 ⁇ M Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent A is added.
- EPHA2 The 2X EPHA2 / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 2.1 - 8.8 ng EPHA2 (or 1.2 – 7.5 ng EPHA5) and 2 ⁇ M Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent B is added.
- TRKA NTRK1
- TRKC TRKC
- the 2X NTRK1 (TRKA) / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 6 - 24 ng NTRK1 (TRKA) or 2.7 – 30 ng NTRK3 (TRKC), and 2 ⁇ M Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- TRKB NTRK2
- the 2X NTRK2 (TRKB) / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 4 mM MnCl 2 , 1 mM EGTA, 2 mM DTT.
- the final 10 ⁇ L Kinase Reaction contains 0.34 - 4 ng NTRK2 (TRKB) and 2 ⁇ M Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 2 mM MnCl2, 1 mM EGTA, 1 mM DTT.
- 5 ⁇ L of a 1:128 dilution of Development Reagent B is added.
- ROS1 The 2X ROS1 / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 3 - 12 ng ROS1 and 2 ⁇ M Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent B is added.
- TNK1 The 2X TNK1 / Ser/Thr 13 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3.
- the final 10 ⁇ L Kinase Reaction contains 15 - 60 ng TNK1 and 2 ⁇ M Ser/Thr 13 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3. After the 1 hour Kinase Reaction incubation, 5 ⁇ L of a 1:1024 dilution of Development Reagent A is added.
- TXK The 2X TXK / Tyr 06 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 4.75 - 19 ng TXK and 2 ⁇ M Tyr 06 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent A is added.
- TYK2 The 2X TYK2 / Tyr 03 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3.
- the final 10 ⁇ L Kinase Reaction contains 3.75 - 15 ng TYK2 and 2 ⁇ M Tyr 03 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3.
- RET The 2X RET / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 0.49 - 3.64 ng RET (or 0.52 – 4.74 ng RET-V804L or 0.86 – 6.16 ng RET-Y791F) and 2 ⁇ M Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent A is added.
- RET-A883F The 2X RET A883F / Tyr 04 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA, 0.02% NaN3.
- the final 10 ⁇ L Kinase Reaction contains 1.02 - 6.74 ng RET-A883F (or 3 – 20 ng RET-V804L) and 2 ⁇ M Tyr 04 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA, 0.01% NaN3.
- RET-S891A The 2X RET S891A / Tyr 06 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 0.3 - 1.4 ng RET- S891A and 2 ⁇ M Tyr 06 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- ABL2 (Arg) The 2X ABL2 (Arg) / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ- 35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 0.42 - 3.13 ng ABL2 (Arg) and 2 ⁇ M Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- PTK2B (FAK2): The 2X PTK2B (FAK2) / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MnCl2, 1 mM EGTA, 2 mM DTT, 0.02% NaN3.
- the final 10 ⁇ L Kinase Reaction contains 5.26 - 34.8 ng PTK2B (FAK2) and 2 ⁇ M Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 5 mM MgCl2, 5 mM MnCl2, 1 mM EGTA, 1 mM DTT, 0.01% NaN3.
- PTK2B Fet al.
- SRC, SRC-N1 The 2X SRC / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction consists of 5 - 20 ng SRC (or 1 – 4.9 ng SRC-N1) and 2 ⁇ M Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent A is added.
- LCK The 2X LCK / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction consists of 8 - 33 ng LCK and 2 ⁇ M Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 ⁇ L of a 1:128 dilution of Development Reagent A is added.
- Table 3 in this Example shows IC 50 values for particular inhibitors of phosphorylation activity for PKs other than ABL1.
- TEC, IRAK3, PLK4, RET-G691S, RET-V804M, RET-M918T, TNK2 (ACK), DDR2- N456S and DDR2-T654M PKs were assayed using the Lantha Screen.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 and 1 mM EGTA.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 and 1 mM EGTA.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl 2 , 1 mM EGTA.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- the Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
- IRAK1 a different type of assay was conducted, known as an AdaptaTM Assay based on ADP formation from ATP hydrolysis. It can be used to measure any type of ATP hydrolysis, including the intrinsic ATPase activity of kinases.
- the substrate is water and not a peptide. This assay is described in Kashem, MA et al. (2007) J. Biomol. Screen.12:70-83.
- the 2X IRAK1 / Histone H3 (1-20) peptide mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ- 35, 10 mM MgCl2, 1 mM EGTA.
- the final 10 ⁇ L Kinase Reaction contains 3.5 - 30.5 ng IRAK1 and 100 ⁇ M Histone H3 (1-20) peptide in 32.5 mM HEPES pH 7.5, 0.005% BRIJ-35, 5 mM MgCl2, 0.5 mM EGTA.
- 5 ⁇ L of Detection Mix is added.
- AdaptaTM Screening Protocol and Assay Conditions (Revised 29 Jan-2021) from SelectScreenTM Biochemical Kinase Profiling Service (World Wide Web URL thermofisher.com/selectscreen).
- Table 4 in this Example shows public database accession numbers for PK polypeptides (“NP” and “AA” prefix accession numbers in the World Wide Web URL ncbi.nlm.nih.gov/protein/ database and “P” prefix accession numbers in the World Wide Web URL uniprot.org/uniprotkb/ database), the epitope tag attached and the purity of the PK utilized in each assay.
- Assay Results The following Table 5 reports IC 50 values obtained for test compounds using the assay described in this Example.
- the IC 50 value for each test compound measured for ABL1(wt) and ABL1 variants is reported in nanomolar (nM) units.
- ABL1 variants were ABL1(T315I), ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L), which are referred to in the following Table 5 of this Example by the amino acid substitution in each ABL1 variant.
- Certain IC 50 values are referenced from publications cited as shown.
- Test compound C1 is described in Example 2 herein.
- Test compounds "CompA” and “CompB” are comparative test compounds identified by the library screening process that identified compound C1.
- Table 5 Test A BL1(wt) G250E Y253F E255K T315I F317L Ratio Compound WT:T315I repore n e ae e a., . n. ncoogy: : . . . .
- Compound C1 was considered an effective inhibitor of ABL1(T315I), ABL1(G250E), ABL1(Y253F) and ABL1(E255K), and a partially effective inhibitor of ABL1(F317L). No other test compound in Table 5 of this Example was considered an effective inhibitor of four ABL1 variants and a partially effective inhibitor of one ABL1 variant. Compound C1 was considered a pan-ABL1 inhibitor according to the IC50 values reported in Table 5 of this Example.
- PK inhibition activity assessments for compounds herein as measured by the labeled peptide cleavage assays (Z’LYTETM assays), fluorescence displacement assay (LanthaScreenTM Eu Kinase Binding Assay) and ADP formation assay (AdaptaTM Assay) described in this Example, are presented in FIG.3 to FIG.10C as an IC50 value and/or as a percent inhibition value.
- a value shown without units in FIG.3 to FIG.10C is an IC50 value in nanomolar (nM) units.
- a value shown as a percentage in FIG.3 to FIG.10C is percent inhibition value typically determined at a 100 nM concentration of test compound.
- FIG.3 to FIG.10C includes the term “Cmpd,” which designates a test compound assessed by an assay.
- FIG.3 to FIG.10C show PK inhibition by compounds determined by peptide cleavage and tracer displacement assays.
- FIG.3 shows inhibition of ABL family PKs.
- FIG.4 shows inhibition of BTK family PKs.
- FIG.5 shows inhibition of AURK family PKs.
- FIG.6 shows inhibition of JAK family PKs.
- FIG.7 shows inhibition of TRK family PKs.
- FIG.8 shows inhibition of RET family PKs.
- FIG.9A shows inhibition of EPH family PKs.
- FIG.9B shows inhibition of TNK family, PLK family and IRAK family PKs.
- FIG.9C shows inhibition of SRC and DDR family PKs.
- FIG.9D shows inhibition of ABL2 and PTK2B PKs.
- FIG.10A shows inhibition of ABL and BTK family PKs.
- FIG.10B shows inhibition of ABL and AURK family PKs.
- FIG.10C shows inhibition of ABL, BTK and AURK family PKs.
- the key at the bottom of FIG.3 is applicable to charts in FIG.4 to FIG.10C.
- the top portion of the key is applicable to percent inhibition values and the bottom portion of the key is applicable to IC 50 values.
- a “*” designation signifies that the corresponding value is an external value (for example, a value from a scientific publication);
- an additional row for a particular test compound within one table signifies a different manufacturing lot of the test compound;
- the first value is obtained at a concentration of 100 nM for the test compound and the second value is obtained at a concentration of 10 nM of the test compound;
- a “Lit + ve” designation signifies that the test compound was reported in an external source as exhibiting an inhibitory activity against the applicable target PK (for example, in a scientific publication);
- a % value and an IC50 value within one cell of a table for particular test compound are separated by brackets or by a comma (a bracket or comma separator serve the same function of separating the % value and the IC50 value).
- the “Cmpd” column includes at the end multiple test compounds designated by a “COM” designation, which designates comparative compounds subject to clinical studies that are commercially available.
- the following “COM” designations are held in reserve: COM4, COM11, COM12, COM13, COM14, COM18, COM24, COM25, COM26 and COM27.
- Example 10 Preparation of C8, C9, C10 and C11 Provided in this Example are processes for preparing compounds C8, C9, C10 and C11 shown in Table A.
- the mixture is placed in a 130°C aluminum block and vigorously stirred for 5 hours.
- the vial is rinsed with excess EtOH, then excess DCM, into a 250 mL round-bottomed (rb) flask.
- the solution is evaporated to an orange-brown oil.
- IPA (10 mL) is added and the mixture heated until the residue dissolved.
- the dark solution is allowed to cool and stir at room temperature for 12 hr.
- the dark brown precipitated solid is recovered by filtration. The product is used without further purification.
- the organic phase is set aside and the aqueous phase is adjusted to pH 12 using solid NaOH.
- the aqueous phase is extracted with iPrOAc.
- the aqueous phase is set aside and the organic phase dried over MgSO 4 , filtered and evaporated to an oil.
- the desired product is purified by flash chromatography, yielding the desired compound.
- the aqueous phase is extracted with iPrOAc.
- the aqueous phase is set aside and the organic phase dried over MgSO 4 , filtered and evaporated to an oil.
- the desired product is purified by flash chromatography, yielding the desired compound.
- THF is added to effect dissolution.
- a solution of 8-(3,5-dimethoxyphenyl)-N- (2-methoxy-5-((methylamino)methyl)phenyl)quinazolin-2-amine in THF is added followed by solid sodium triacetoxybotohydride.
- Acetic acid is added and the vial sealed, then stirred at rt for 16 hours.
- the reaction is diluted with excess iPrOAc and filtered.
- the filtrate is washed with 1N aqueous sodium hydroxide (2x washes).
- the organic phase is washed with aqueous 1N HCl (2x washes).
- the organic phase is set aside and the aqueous phase is adjusted to pH 12 using solid NaOH.
- Example 11 9H-fluoren-9-ylmethyl N-[5-(tert-butoxycarbonylamino)-2-methyl- phenyl]carbamate (Compound A)
- Examples 11-14 are for preparing C12.
- this Example 11 provided is a process for preparing a compound having the following structure: H H N N .
- a 250 mL round bottom flask with stir bar was charged with DCM (50 mL).
- Example 12 9H-fluoren-9-ylmethyl N-(5-amino-2-methyl-phenyl)carbamate hydrochloride (Compound B)
- the compound having the following structure was prepared: . (rb) flask containing 9H-fluoren-9-ylmethyl N-[5-(tert- butoxycarbonylamino)-2-methyl-phenyl]carbamate was charged with DCM (50 mL). TFA (10 mL) was added and the yellow suspension became homogenous and turned dark brown in 1 hour (hr). The solution was stirred at room temperature overnight. Toluene (20 mL) was added, and the reaction evaporated to a dark residue (9.205 g).
- Example 13 9H-fluoren-9-ylmethyl N-[5-[(8-bromoquinazolin-2-yl)amino]-2-methyl- phenyl]carbamate (Compound C)
- the compound having the following structure was prepared: . – with stir bars were each charged with [3-(9H-fluoren-9- ylmethoxycarbonylamino)-4-methyl-phenyl]ammonium;chloride (526 mg, 1.381 mmol).
- Dioxane (10 mL) was added to each vial and the mixture stirred for 5 min to effect complete suspension. While stirring, each vial was then charged with 8-bromo-2-chloro-quinazoline (673 mg, 2.762 mmol).
- Example 14 4-((2-methyl-5-((8-phenylquinazolin-2-yl)amino)phenyl)carbamoyl)benzoic acid
- the title compound having the following structure was prepared (C12): .
- the mixture containing a yellow solid suspended in the two-phase dioxane/water solvent, was poured into iPrOAc ( ⁇ 100 mL). The solid dissolved. The mixture was transferred to a separatory funnel and the lower aqueous was removed and set aside. The clear, brown organic was dried over MgSO4 and filtered into a 250 mL rb flask. The filtrate was evaporated down to about 50 mL volume, then treated with 1N HCl (50 mL). The orange mixture was vigorously stirred overnight. The two-phase mixture consisted of a deep yellow aqueous phase and a brown organic phase with a small amount of insoluble residue floating at the interface. The mixture was transferred to a separatory funnel.
- ethyl 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoate as a yellow/orange solid (490 mg).
- a 10 - 20 mL microwave vial was charged with ethyl 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoate.
- Tetrahydrofuran (THF) was added and the mixture stirred for 1 min to effect full suspension.
- Example 15 Preparation of C13 A nucleophilic aromatic substitution (SNAr) was performed: with ethyl 4-((3-amino- 4-methylphenyl)carbamoyl)benzoate (189 mg, 0.63 mmol). EtOH (3.17 mL) was added and the mixture stirred until significant dissolution was obtained.8-bromo-2-chloro-quinazoline (309 mg, 1.27 mmol) was added. The vial was sealed and heated, with stirring, in an aluminum block (120°C) for 5 hours. The reaction was poured into excess iPrOAc and washed with sat aq sodium bicarbonate (3x). The organic layer was dried over MgSO 4 , filtered and concentrated under reduced pressure.
- SNAr nucleophilic aromatic substitution
- Tetrakis(triphenylphosphine)palladium (8.55 mg, 0.007 mmol) was added, and the vial sealed, then heated in an aluminum block (105°C) for 5 hours. The reaction was diluted with excess iPrOAc and dried over MgSO 4 . Filtration and evaporation afforded a yellow solid. The crude material was purified by pTLC (40:1 CH 2 Cl 2 :MeOH). One band was isolated containing pure product (5.7 mg, 39% yield).
- Example 16 Preparation of C14 An Fmoc protection was performed: with tert-butyl (3-amino-4- ethylphenyl)carbamate (1.072 g, 4.82 mmol). DCM (20 mL) was added and the mixture stirred until dissolution was complete.
- the reaction which was still a white suspension, was poured into a vigorously stirred mixture of saturated bicarb and iPrOAc.
- the white suspension did not dissolve after stirring for 15 min.
- the mixture was transferred to a 500 mL separation funnel with liberal iPrOAc rinsing.
- the slightly turbid, colorless aqueous phase was removed and the organic white suspension was washed twice more with bicarbonate and then water.
- the aqueous layers were removed each time without any significant emulsification.
- the organic phase was allowed to stand overnight in the separation funnel. There was a layer of white suspended material beneath a clear supernatant.
- the white flocculent material was mostly recovered and temporarily set aside.
- LCMS showed somewhat less recovered starting material. The peak at 5.15 no longer showed the 521.206 mass peak. The peak at 4.12 corresponded to the theoretical mass and isotopic distribution of the aniline product resulting from loss of Fmoc from the initial amidation reaction.
- the reaction was partitioned between excess iPrOAc and saturated bicarbonate. The organic phase was washed with bicarbonate (2x more), then water (no acid wash). The organic phase was dried over MgSO4, filtered and evaporated to a dark oil (726 mg). The oil was dissolved in iPrOAc and washed with 1N HCl (3x wash). The aqueous phase was sampled for LCMS and showed the deprotected product in usable condition.
- aqueous phase was layered with excess iPrOAc and basified with solid NaHCO3.
- the organic phase was recovered, dried over MgSO4, filtered and evaporated to a dark residue (304 mg), which was used in the next step.
- a nucleophilic aromatic substitution (SNAr) then was performed: - charged with ethyl 4-[(3-amino-4-methyl-phenyl)carbamoyl]benzoate (304 mg total, 1.019 mmol).
- EtOH 6.0 mL total
- 8-bromo-2-chloro-quinazoline 1.241 g, 5.095 mmol.
- the mixtures were heated in an aluminum block (125°C) for a total of 4 hours.
- LCMS shows the reaction is complete and the desired product is present in all three vials.
- the reaction mixtures from the three vials were combined and evaporated to a yellow solid.
- the solid was digested in IPA at reflux, then stirred overnight at room temperature.
- the light brown solid was recovered by filtration (1.010 g).
- the solid was suspended in DCM (5 mL). Not all of it dissolved.
- the clear orange/brown supernatant was loaded onto a 24g normal phase column and eluted with a DCM/MeOH gradient (0% to 10% MeOH in DCM, 7 column volumes, then 10% MeOH in DCM 6 column volumes). The more retained peak was collected (54 mg obtained).
- the vial was sealed and heated for 8 hours in an aluminum block (85°C) while stirring.
- the yellow mixture was treated with 1N HCl (2 mL).
- the suspended solid initially dissolved but with further stirring a new solid precipitated.
- the mixture was transferred to a 40 mL screw top vial and the organics evaporated.
- the water and solid mixture was diluted with more water (2 mL) and brought to a boil, then allowed to cool with the vial clamped at an angle such that the solid could settle to the bottom of the mixture and leave the supernatant above.
- the slightly turbid supernatant was drawn off by a syringe.
- the procedure was repeated two more times.
- the wet solid was lyophilized overnight resulting in a light yellow solid (37 mg).
- the term “about” as used herein refers to a value within 10% of the underlying parameter (i.e., plus or minus 10%; e.g., a weight of “about 100 grams” can include a weight between 90 grams and 110 grams).
- Use of the term “about” at the beginning of a listing of values modifies each of the values (e.g., “about 1, 2 and 3” refers to "about 1, about 2 and about 3").
- the listing includes all intermediate values and all fractional values thereof (e.g., the listing of values "80%, 85% or 90%” includes the intermediate value 86% and the fractional value 86.4%).
Landscapes
- Chemical & Material Sciences (AREA)
- Organic Chemistry (AREA)
- Health & Medical Sciences (AREA)
- Chemical Kinetics & Catalysis (AREA)
- General Chemical & Material Sciences (AREA)
- Medicinal Chemistry (AREA)
- Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
- Pharmacology & Pharmacy (AREA)
- Life Sciences & Earth Sciences (AREA)
- Animal Behavior & Ethology (AREA)
- General Health & Medical Sciences (AREA)
- Public Health (AREA)
- Veterinary Medicine (AREA)
- Oncology (AREA)
- Hematology (AREA)
- Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
Abstract
Provided in part herein are protein kinase inhibitors having a structure according to specified Formulae, and use thereof.
Description
PROTEIN KINASE INHIBITORS AND USES THEREOF Related application This patent application is related to U.S. provisional patent application no.63/488,429, filed on March 3, 2023, entitled PROTEIN TYROSINE KINASE INHIBITORS, naming Kevin SLAWIN et al. as inventors, and designated by attorney docket no.061897-501P01US and to U.S. provisional patent application no.63/554,855, filed on February 16, 2024, entitled PROTEIN KINASE INHIBITORS AND USES THEREOF, naming Kevin SLAWIN et al. as inventors, and designated by attorney docket no.055337.0001US02. The entire content of both of the foregoing patent applications are incorporated herein by reference for all purposes, including all text, tables and drawings. Reference to a Sequence Listing This application contains a Sequence Listing in computer readable form with file name 05337.0001WO01.xml (created February 29, 2024, 13 kb). The computer readable form is incorporated herein by reference. Field The technology relates in part to compounds that contain a quinazolinyl group and an amine-linked phenyl group. Compounds herein can inhibit one or more protein kinases (PKs), and the technology relates in part to uses of compounds herein. Background Protein kinases (PKs) are a category of proteins that catalyze phosphorylation of different protein substrates. Each PK typically is referred to by the three or four letter code afforded to the gene that encodes the PK protein. PKs are categorized into PK families according to polypeptide sequence and/or function. Dysregulation of PK genes and their encoded PKs are associated with certain cancers. The ABL1 protooncogene, for example, which also is known as ABL, JTK7, p150, c-ABL, CHDSKM, c-ABL1, encodes an ABL1 PK implicated in processes of cell differentiation, cell division, cell adhesion, and stress response. Activity of the ABL1 PK is negatively regulated by its SH3 polypeptide domain. Modification to the ABL1 protooncogene, such as deletion of the SH3 domain-encoding portion and fusion with another protein, for example, can turn it into an oncogene. Translocation and head-to-tail fusion of the BCR and ABL1 genes is present in cases of chronic myeloid leukemia (CML) and in a subset of acute lymphoblastic leukemia (i.e., Philadelphia chromosome-positive ALL). Genes encoding other PKs, which can phosphorylate protein targets different than those of ABL1, can be dysregulated in certain cancers and other medical conditions.
Summary Provided are compounds that inhibit one or more particular PKs, including ABL, BTK, AURK, JAK, TRK, RET, EPH, TNK, PLK, IRAK and TYK family PKs, and may be used for treating cancers and other medical conditions. Compounds herein contain a quinazolinyl group, an amine-linked phenyl group and substituents that can afford PK inhibitory activity. Compounds herein can inhibit multiple PKs in certain embodiments. Compounds herein can selectively inhibit at least one PK in certain instances. Compounds that inhibit one or more particular protein kinases (PKs) can be used to treat cancers and other medical conditions. Brief Description of the Drawings The drawings illustrate certain implementations of the technology and are not limiting. For clarity and ease of illustration, the drawings are not made to scale, and, in some instances, various aspects may be shown exaggerated or enlarged to facilitate an understanding of particular implementations. FIG.1 illustrates processes of a fluorescence-based PTK substrate peptide assay. FIG.2 illustrates amino acid substitutions identified in certain ABL1 variants. FIG.3 to FIG.10C show PK inhibition by compounds determined by peptide cleavage and tracer displacement assays. FIG.3 shows inhibition of ABL family PKs. FIG.4 shows inhibition of BTK family PKs. FIG.5 shows inhibition of AURK family PKs. FIG.6 shows inhibition of JAK family PKs. FIG.7 shows inhibition of TRK family PKs. FIG.8 shows inhibition of RET family PKs. FIG.9A shows inhibition of EPH family PKs. FIG. 9B shows inhibition of TNK family, PLK family and IRAK family PKs. FIG.9C shows inhibition of SRC and DDR family PKs. FIG.9D shows inhibition of ABL2 and PTK2B PKs. FIG.10A shows inhibition of ABL and BTK family PKs. FIG.10B shows inhibition of ABL and AURK family PKs. FIG. 10C shows inhibition of ABL, BTK and AURK family PKs. The legend at the bottom of FIG.3 is applicable to charts in FIG.4 to FIG.10C. Detailed Description Compounds herein can inhibit one or more protein kinases (PKs) and can be used for treatment of medical conditions including cancers. Development of PK inhibitor cancer treatments is challenging. PK inhibitor drugs can present issues including ineffectiveness in a patient subgroup, loss of therapeutic effect during treatment for a patient subgroup, and triggering a serious adverse event in a patient subgroup. For example, an amino acid substitution in the ABL1 kinase domain occurring in a patient can impart resistance to cancer treatment. An ABL1 variant containing a threonine 315 to isoleucine (T315I) amino acid substitution can result in resistance to cancer treatment, for example. It has been reported that developing inhibitors against this variant is challenging because inhibitor candidates often bind to the PK at or near the site of the amino acid
substitution. Despite this challenge, certain compounds herein can effectively inhibit the ABL1(T315I) variant. Certain compounds herein can effectively inhibit other PKs, can effectively inhibit multiple PKs in different PK families and/or can selectively inhibit a PK. Compounds In certain implementations, provided is a compound of Formula A: R2 R1 R3 Formula A
where: R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R4, R5 and R6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo. In certain instances, R1, R2 and R3 each independently is hydrogen, methyl or methoxy. In certain instances, R4, R5 and R6 each independently is hydrogen, fluoro, chloro, isopropyl, or isopropyloxy. In certain instances, one of R1, R2 and R3 is methyl or methoxy and the other two of R1, R2 and R3 each is hydrogen. In certain instances, R1 is methyl or methoxy and R2 and R3 each is hydrogen. In certain embodiments, R1 is methyl and R2 and R3 each is hydrogen. In certain instances, R3 is methyl or methoxy and R1 and R2 each is hydrogen. In certain embodiments, R3 is methyl and R1 and R2 each is hydrogen. In certain instances, R1, R2 and R3 each is hydrogen, and sometimes R5 is hydrogen. In certain embodiments, R4, R5 and R6 each is hydrogen. In certain implementations, provided is a compound of Formula B: R2 Formula B
or a pharmaceutically acceptable salt thereof, where:
R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R7, R8 and R9 each independently is hydrogen or optionally substituted C1-C6 alkyl. In certain instances, R1, R2 and R3 each independently is hydrogen, methyl or methoxy. In certain instances, R7, R8 and R9 each independently is hydrogen or isobutyl. In certain instances, one of R1, R2 and R3 is methyl or methoxy and the other two of R1, R2 and R3 are hydrogen. In certain instances, R1, R2 and R3 each is hydrogen, and sometimes R8 and R9 each is hydrogen. In certain implementations, provided is a compound of Formula C: R2 R1 R3 Formula C
R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R10, R11, R12 and R13 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy; m is an integer of 1 or 2; R14 is methyl or O ;
1 to 10; and R15 is hydrogen, optionally substituted alkyl or optionally substituted amidoalkyl. It is understood that where m is the integer of 1, the nitrogen bound to the R47 has a covalently bound hydrogen, as depicted in Formula D. In certain instances, m is the integer 1 and the compound is of Formula D:
R2 R1 R3 N Formula D
each independently is hydrogen, methyl or methoxy. In certain instances, one of R1, R2 and R3 is methyl or methoxy and the other two of R1, R2 and R3 are hydrogen. In certain instances, R1, R2 and R3 each is hydrogen. In certain instances, R10, R11, R12 and R13 each independently is hydrogen or methoxy. In certain instances, R10 and R12 each is hydrogen, and sometimes R11 and R13 each is methoxy. In certain instances, m is the integer 2. In certain instances, R14 is O .
n is an integer of 3 to 7. In certain aspects, provided is a compound of the following Subgroup 1, Subgroup 2 or Subgroup 3. A Subgroup 1 compound is of Formula A, where R1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R2, R3 and R5 each is hydrogen; and R4 and R6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo, with the proviso that R4 or R6 , or R4 and R6, is not hydrogen. In certain embodiments, R1 is an unsubstituted C1-C4 alkyl, ethyl or methyl. In certain embodiments, (i) R4 is unsubstituted C1-C4 alkoxy or isopropyloxy; (ii) R6 is fluoro or chloro; or a combination of (i) and (ii). In certain embodiments, a Subgroup 1 compound is 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2- yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C1); 4-((5-((8-(4-fluoro-2- isopropoxyphenyl)quinazolin-2-yl)amino)-2-methoxyphenyl)carbamoyl)benzoic acid (compound C3); 4-((5-((8-(2-isopropylphenyl)quinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C4); or a pharmaceutically acceptable salt thereof. A Subgroup 2 compound is of Formula A, where R1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R2, R3, R4, R5 and R6 each is hydrogen. In certain embodiments, R1 is an unsubstituted C1-C4 alkyl, ethyl or methyl. In certain embodiments, a Subgroup 2 compound is 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid (compound C12) or a pharmaceutically acceptable salt thereof.
A Subgroup 3 compound is of Formula A, where R3 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R1, R2, R4, R5 and R6 each is hydrogen. In certain embodiments, R3 is an unsubstituted C1-C4 alkyl, ethyl or methyl. In certain embodiments, a Subgroup 3 compound is 4-((4-methyl-3-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid (compound C13) or a pharmaceutically acceptable salt thereof. In certain implementations, a compound is of Formula C or Formula D with the proviso that R12 is not methoxy. In certain implementations, a composition contains a compound of Formula C or Formula D with the proviso that R12 is not O N O O S .
a compound of Formula C or Formula D with the proviso that R11 or R13 is not O .
a composition contains a compound according to Formula A, Formula B, Formula C or Formula D with the proviso that R1 and R2, or optionally R2 and R3, do not join to form an imidazolyl group. In certain embodiments, a composition contains a compound according to Formula A, Formula B, Formula C or Formula D with the proviso that R1 and R2, or optionally R2 and R3, are not joined as: (i) an imidazolyl moiety fused to the phenyl group on which R2, R3 and R4 are substituents; (ii) an indolyl group; (iii) a five-membered ring; (iv) a five-membered ring fused to the phenyl group on which R1, R2 and R3 are substituents; (v) unsubstituted heteroaryl containing 5 ring atoms; and/or (vi) substituted heteroaryl containing 5 ring atoms. In certain embodiments, a composition contains a compound according to Formula A, Formula B, Formula C or Formula D with the proviso that R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, R12, R13, R14 or R15 each independently is not: (i) one of the following designated Group A electrophilic groups:
; (ii) one of the following designated Group B electrophilic groups: ;
and/or (iii) an electrophilic group capable of forming a covalent bond with a cysteine of a protein. In certain embodiments, a compound herein is provided as a hydrochloride salt. In certain implementations, a composition contains a compound, or a combination of two or more of the compounds, described in the following Table A (the term "Compound" is abbreviated by "Cmpd" in the header row of Table A).
Table A Cmpd Structure Name (IUPAC) d d id
Cmpd Structure Name (IUPAC) - n- - id id
Cmpd Structure Name (IUPAC)
In certain implementations, a composition described herein is provided as a pharmaceutical composition. In certain implementations, a compound in a composition described herein binds to an ABL1 polypeptide. In certain instances, a compound in a composition described herein inhibits an activity of an ABL1 polypeptide. In certain instances, a compound binds to two or more ABL1 variant polypeptides. In certain instances, a compound inhibits an activity of two or more ABL1 variant polypeptides. In certain implementations, a compound is an effective inhibitor of two or more ABL1 variant polypeptides. In certain implementations, a composition described herein is for inhibition of an activity of an ABL1 polypeptide or ABL1 variant polypeptide. In certain instances, a composition described herein is for inhibition of a catalytic activity of an ABL1 polypeptide or ABL1 variant polypeptide. In certain instances, a composition described herein is for treatment of a condition, which sometimes is an ABL1-related condition. In certain instances, the condition is a cancer, and sometimes the cancer is a leukemia. In certain instances, the leukemia is chronic myeloid leukemia or acute lymphoblastic leukemia. In the context of a chemical structure, a reference to a chemical structure, or a structure provided as part of a synthetic scheme, a number or letter normally designated as a superscript, for example, the “1” in R1, or the “L” in RL, may be referred to as a subscript, for example, R1 or RL, or without any modification of script, such as, for example, R1 or RL. Any definition herein may be used in combination with any other definition to describe a composite structural group. By convention, the trailing element of any such definition is that which attaches to a parent moiety. The composite group alkylamido, for example, would represent an alkyl group attached to a parent molecule through an amido group, the term amidoalkyl would represent an amido group attached to a parent molecule through an alkyl group, the term alkylalkoxy would represent an alkyl group attached to a parent molecule through an alkoxy group, and the term alkoxyalkyl would represent an alkoxy group attached to a parent molecule through an alkyl group, for example.
When a group is defined to be “null,” the group is absent. The term “optionally substituted” means the anteceding group may be substituted or unsubstituted. The term “substituted,” as used herein, refers, without limitation, to one or more substituents that can include, for example, substituents independently selected from the following groups or a particular designated set of groups, alone or in combination: lower alkyl, lower alkenyl, lower alkynyl, lower alkanoyl, lower heteroalkyl, lower aryl, lower cycloalkyl, lower heteroaryl, lower heterocycloalkyl, aryl, cycloalkyl, heteroaryl, heterocycloalkyl, lower haloalkyl, lower haloalkenyl, lower haloalkynyl, lower perhaloalkyl, lower perhaloalkoxy, phenyl, aryloxy, lower hydroxyalkyl, lower mercaptoalkyl, lower aminoalkyl, lower arylaminoalkyl, aryloxyalkyl, lower aryloxyalkyl, arylthioalkyl, lower arylthioalkyl, heteroarylaminoalkyl, heteroaryloxyalkyl, heteroarylthioalkyl, arylalkyl, lower arylalkyl, heteroarylalkyl, lower heteroarylalkyl, lower alkoxy, lower haloalkoxy, oxo, lower acyloxy, carbonyl, carboxyl, lower alkylcarbonyl, lower carboxyester, lower carboxamido, cyano, hydrogen, halogen, hydroxy, amino, lower alkylamino, arylamino, amido, nitro, thiol, lower alkylthio, lower haloalkylthio, lower perhaloalkylthio, arylthio, sulfonate, sulfonic acid, trisubstituted silyl, N3, SH, SCH3, C(O)CH3, CO2CH3, CO2H, B(OH)2, pyridinyl, thiophene, furanyl, lower carbamate, and lower urea. Two substituents may be joined together to form a fused five-, six-, or seven-membered carbocyclic, heterocyclic aryl, or heteroaryl ring system having zero to three heteroatoms, for example, forming methylenedioxy or ethylenedioxy. An optionally substituted group may contain a deuterium in place of one or more hydrogen atoms (e.g., -CD3 instead of -CH3). An optionally substituted group may be unsubstituted (e.g., -CH2CH3), fully substituted (e.g., -CF2CF3), monosubstituted (e.g., - CH2CH2F) or substituted at a level anywhere in-between fully substituted and monosubstituted (e.g., -CH2CF3). Where substituents are recited without qualification as to substitution, both substituted and unsubstituted forms are encompassed. Where a substituent is qualified as “substituted,” the substituted form is specifically intended. Additionally, different sets of optional substituents to a particular moiety may be defined as needed. An optional substitution often is as defined, sometimes immediately following the phrase, “optionally substituted with.” The term R or the term R’, appearing by itself and without a number designation, unless otherwise defined, refers to a moiety chosen from hydrogen (H), alkyl, cycloalkyl, heteroalkyl, aryl, heteroaryl and heterocycloalkyl, any of which may be optionally substituted. Such R and R’ groups should be understood to be optionally substituted as defined herein. Whether an R group has a number designation or not, every R group, including R, R’ and Rn where n = (1, 2, 3, …n), every substituent, and every term should be understood to be independent of every other in terms of selection from a group. Should any variable, substituent, or term (e.g. aryl, heterocycle, R, etc.) occur more than one time in a formula or generic structure, its definition at each occurrence is independent of the definition at every other occurrence. Certain groups may be attached to a
parent molecule or may occupy a position in a chain of elements from either end as written. Thus, by way of example only, an asymmetrical group such as –C(O)N(R)– may be attached to a parent moiety at either the carbon or the nitrogen. In embodiments, the term ‘substituted’ and ‘substituent group’, as used herein, means a group selected from the following moieties: (A) oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, –OSO3H, -SO2NH2, −NHNH2, −ONH2, −NHC(O)NHNH2, −NHC(O)NH2, – NHC(NH)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -N3, -SF5, unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), and (B) alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: (i) oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, –OSO3H, -SO2NH2, −NHNH2, −ONH2, −NHC(O)NHNH2, −NHC(O)NH2, –NHC(NH)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -N3, -SF5, unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered
heterocycloalkyl), unsubstituted aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), and (ii) alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: (a) oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCH F2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, - SO3H, –OSO3H, -SO2NH2, −NHNH2, −ONH2, −NHC(O)NHNH2, −NHC(O)NH2, – NHC(NH)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -N3, -SF5, unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), and (b) alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1-C4 alkyl), heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl), substituted with at least one substituent selected from: oxo, halogen, -CCl3, -CBr3, -CF3, -CI3, -CHCl2, -CHBr2, -CHF2, -CHI2, -CH2Cl, -CH2Br, -CH2F, -CH2I, -OCCl3, -OCF3, -OCBr3, -OCI3, -OCHCl2, -OCHBr2, -OCHI2, -OCHF2, -OCH2Cl, -OCH2Br, -OCH2I, -OCH2F, -CN, -OH, -NH2, -COOH, -CONH2, -NO2, -SH, -SO3H, –OSO3H, -SO2NH2, −NHNH2, −ONH2,
−NHC(O)NHNH2, −NHC(O)NH2, –NHC(NH)NH2, -NHSO2H, -NHC(O)H, -NHC(O)OH, -NHOH, -N3, -SF5, unsubstituted alkyl (e.g., C1-C8 alkyl, C1-C6 alkyl, or C1- C4 alkyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered heteroalkyl), unsubstituted cycloalkyl (e.g., C3-C8 cycloalkyl, C3-C6 cycloalkyl, or C5-C6 cycloalkyl), unsubstituted heterocycloalkyl (e.g., 3 to 8 membered heterocycloalkyl, 3 to 6 membered heterocycloalkyl, or 5 to 6 membered heterocycloalkyl), unsubstituted aryl (e.g., C6-C10 aryl, C10 aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl). A “size-limited substituent” or “size-limited substituent group,” as used herein, means a group selected from all of the substituents described above for a “substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl. A “lower substituent” or “lower substituent group,” as used herein, means a group selected from all of the substituents described above for a “substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted phenyl, and each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 6 membered heteroaryl. In some embodiments, each substituted group described in the compounds herein is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In some embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group.
In some embodiments, at least one or all of these groups are substituted with at least one lower substituent group. In some embodiments of the compounds herein, each substituted or unsubstituted alkyl may be a substituted or unsubstituted C1-C20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and/or each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl. In some embodiments of the compounds herein, each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C20 alkylene, each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered heteroalkylene, each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C8 cycloalkylene, each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene, each substituted or unsubstituted arylene is a substituted or unsubstituted C6- C10 arylene, and/or each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered heteroarylene. In some embodiments, each substituted or unsubstituted alkyl is a substituted or unsubstituted C1- C8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C3-C7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C6-C10 aryl, and/or each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl. In some embodiments, each substituted or unsubstituted alkylene is a substituted or unsubstituted C1-C8 alkylene, each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene, each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C3-C7 cycloalkylene, each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene, each substituted or unsubstituted arylene is a substituted or unsubstituted C6-C10 arylene, and/or each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene. In some embodiments, the compound is a chemical species set forth in the Examples section, figures, or tables below. In embodiments, a substituted or unsubstituted moiety (e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is unsubstituted (e.g., is an unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, unsubstituted alkylene, unsubstituted heteroalkylene, unsubstituted cycloalkylene, unsubstituted heterocycloalkylene, unsubstituted arylene, and/or unsubstituted heteroarylene, respectively). In embodiments, a substituted or unsubstituted moiety (e.g., substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, and/or substituted or unsubstituted heteroarylene) is substituted (e.g., is a substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene, respectively). In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one substituent group, wherein if the substituted moiety is substituted with a plurality of substituent groups, each substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of substituent groups, each substituent group is different. In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one size-limited substituent group, wherein if the substituted moiety is substituted with a plurality of size-limited substituent groups, each size-limited substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of size-limited substituent groups, each size-limited substituent group is different.
In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one lower substituent group, wherein if the substituted moiety is substituted with a plurality of lower substituent groups, each lower substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of lower substituent groups, each lower substituent group is different. In embodiments, a substituted moiety (e.g., substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene) is substituted with at least one substituent group, size-limited substituent group, or lower substituent group; wherein if the substituted moiety is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group may optionally be different. In embodiments, if the substituted moiety is substituted with a plurality of groups selected from substituent groups, size-limited substituent groups, and lower substituent groups; each substituent group, size-limited substituent group, and/or lower substituent group is different. The term “alkoxy,” as used herein, alone or in combination, refers to an alkyl ether radical, where the term alkyl is as defined below. Non-limiting examples of alkyl ether radicals include methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, and the like. The term “alkyl,” as used herein, alone or in combination, refers to a saturated straight-chain or branched-chain hydrocarbon radical containing from 1 to 20 carbon atoms. The term “straight-chain alkyl” refers to a saturated straight-chain hydrocarbon radical. The term “branched-chain alkyl” refers to a saturated branched-chain hydrocarbon radical. In certain embodiments, an alkyl includes 1 to 10 carbon atoms (C1-C10 alkyl), 1 to 8 carbon atoms (C1-C8 alkyl), 1 to 6 carbon atoms (C1-C6 alkyl) or 1 to 3 carbon atoms (C1-C3 alkyl). Alkyl groups may be optionally substituted as defined herein. Non-limiting examples of alkyl radicals include methyl, ethyl, n- propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl, nonyl and the like. The term “alkylene,” as used herein, alone or in combination, refers to a saturated aliphatic group derived from a straight or branched chain saturated hydrocarbon attached at two or more positions,
such as methylene (–CH2–). Unless otherwise specified, the term “alkyl” may include “alkylene” groups. The term “alkylamino,” as used herein, alone or in combination, refers to an alkyl group attached to a parent molecular moiety through an amino group. Alkylamino groups include monoalkylated groups (monoalkylamino) or dialkylated groups (dialkylamino), non-limiting examples of which include N-methylamino, N-ethylamino, N,N-dimethylamino, N,N-ethylmethylamino and the like. The terms “amido” and “carbamoyl,” as used herein, alone or in combination, refer to an amino group as described below attached to a parent molecular moiety through a carbonyl group, or vice versa. The term “C-amido” as used herein, alone or in combination, refers to a -C(O)N(RR’) group with R and R’ as defined herein or as defined by the specifically enumerated “R” groups designated. The term “N-amido” as used herein, alone or in combination, refers to a RC(O)N(R’)- group, with R and R’ as defined herein or as defined by the specifically enumerated “R” groups designated. The term "acylamino" as used herein, alone or in combination, includes an acyl group attached to a parent moiety through an amino group. A non-limiting example of an "acylamino" group is acetylamino (CH3C(O)NH–). The term “amino,” as used herein, alone or in combination, refers to -NRR’, where R and R’ are independently chosen from hydrogen, alkyl, alkenyl, alkynyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R’ may combine to form heterocycloalkyl or heteroaryl, either of which may be optionally substituted. The term "aminoalkyl," as used herein, refers to an amino group attached to a parent molecule through an alkyl group (N(R)(R')-alkyl-), where R and R' are defined herein. The term "lower aminoalkyl," as used herein, refers to an amino group attached to a parent molecule through a lower alkyl group (N(R)(R')-lower alkyl-), where "lower alkyl," R and R' are defined herein. The term "aryl," as used herein, alone or in combination, refers to an aromatic cyclic ring system, or aromatic hydrocarbon ring system, in which all of the atoms that form the covalent structure of the one or more aromatic rings are carbon (referred to herein as an “aryl ring”). The aryl ring may be optionally substituted as defined herein. The ring system may be monocyclic or fused polycyclic, for example, bicyclic or tricylic (containing two or three rings fused together). In certain embodiments, the monocyclic aryl ring is C4-C10, or C5-C9, or C5-C8, or C5-C7, or, in certain embodiments, C5- C6, where these carbon numbers refer to the number of carbon ring member atoms that form the ring system. In some embodiments, the polycyclic ring system is a bicyclic aryl group, where the bicyclic aryl group in some embodiments is C8-C12, or, for example, C9-C10. In some embodiments, the polycyclic ring system is a tricyclic aryl group, where the tricyclic aryl group is
C11-C18, or, for example, C12-C16. Non-limiting examples of aryl ring systems include phenyl (monocyclic, C6), naphthyl (bicyclic, C10), anthracenyl (tricyclic, C14) and phenanthryl (tricyclic, C14). The term “arylalkyl” or “aralkyl,” as used herein, alone or in combination, refers to an aryl group attached to a parent molecular moiety through an alkyl group. The term “lower arylalkyl” or “lower aralkyl,” as used herein, alone or in combination, refers to a lower aryl group attached to a parent molecular moiety through a lower alkyl group, where "lower aryl" and "lower alkyl" are as defined herein. The term “arylalkynyl” or “aralkynyl,” as used herein, alone or in combination, refers to an aryl group attached to a parent molecular moiety through an alkynyl group. The term "arylaminoalkyl" as used herein refers to an aryl group attached to a parent molecule through an aminoalkyl group (aryl-N(R)-alkyl-), where R is as defined herein. The term "lower arylaminoalkyl" as used herein refers to a lower aryl group attached to a parent molecule through a lower aminoalkyl group (lower aryl-N(R)-lower alkyl-), where "lower aryl," "lower aminoalkyl" and R are as defined herein. The terms “benzo” and “benz,” as used herein, alone or in combination, refer to the divalent radical C6H4= derived from benzene. Non-limiting examples include benzothiophene and benzimidazole. The term “carbamate,” as used herein, alone or in combination, refers to an ester of carbamic acid (–NHCOO–) which may be attached to a parent molecular moiety from either the nitrogen or acid end, and which may be optionally substituted as defined herein. The term “O-carbamyl” as used herein, alone or in combination, refers to a -OC(O)NRR’ group where R and R’ are as defined herein. The term “N-carbamyl” as used herein, alone or in combination, refers to a ROC(O)NR’- group, where R and R’ are defined herein. The term “carbonyl,” as used herein, when alone includes formyl [–C(O)H] and in combination includes a –C(O)– group. The term “carboxyl” or “carboxy,” as used herein, refers to –C(O)OH or the corresponding “carboxylate” anion (e.g., in a carboxylic acid salt). An “O-carboxy” group refers to a RC(O)O– group, where R is as defined herein. A “C-carboxy” group refers to a –C(O)OR group where R is as defined herein. The terms “cycloalkyl,” and, interchangeably, “carbocycle,” as used herein, alone or in combination, refers to a ring system in which all of the ring member atoms are carbon and at least one of the
rings is a saturated or partially unsaturated aliphatic cyclic ring moiety (referred to herein as a “cycloalkyl ring” or “carbocycle ring”). In some embodiments, each cyclic moiety contains from 3 to 12 carbon ring member atoms which may be optionally substituted as defined herein. In some embodiments, a cycloalkyl group contains 3 to 10 carbon ring member atoms. In certain embodiments, a cycloalkyl includes 5 to 7 carbon atoms. In certain embodiments, a cycloalkyl includes 5 to 6 carbon atoms. A cycloalkyl can be a monocyclic or polycyclic, e.g., bicyclic or tricyclic, ring system in which at least one cyclic ring is a cycloalkyl ring. In certain embodiments, the monocyclic cycloalkyl ring is C3-C10, or C5-C9, or C5-C8, or C5-C7, or, in certain embodiments, C5-C6, where these carbon numbers refer to the number of carbon ring member atoms that form the ring system. Polycyclic cycloalkyl ring systems include fused, bridged and spiro-fused rings. Polycyclic cycloalkyl ring systems as defined herein, include ring systems in which one or more cycloalkyl rings is/are fused to one or more aryl rings (benzo-fused cycloalkyl ring systems) and/or other cycloalkyl rings. In some embodiments, all of the rings in a polycyclic cycloalkyl ring system are cycloalkyl rings. In some embodiments, the polycyclic ring system is a bicyclic cycloalkyl group, where the bicyclic cycloalkyl group in some embodiments is C8-C12, or, for example, C9-C10. In some embodiments, the polycyclic ring system is a tricyclic cycloalkyl group, where the tricyclic cycloalkyl group is C11-C18, or, for example, C12-C16. Non-limiting examples of such cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, octahydronaphthalene, decahydronaphthalene, bicyclo[1,1,1]pentane and the like. Examples of aryl-fused cyclolalkyl ring systems include a benzene ring fused to hydrogenated or partially hydrogenated ring systems, non-limiting examples of which include dihydronaphthalene, tetrahydronaphthalene and indanyl. In polycyclic systems in which a cycloalkyl is fused to an aryl, attachment of the polycycle to the indicated point of attachment on the parent molecule may be through any ring atom of the polycycle rings. In some embodiments of polycyclic cycloalkyls, the polycycle is attached to the indicated point of attachment through a ring member atom of a cycloalkyl ring. In some embodiments of polycyclic cycloalkyls, the polycycle is attached to the indicated point of attachment through a ring member atom of a ring that is not a cycloalkyl ring, e.g., an aryl ring. The term “carbocycle-alkyl” or “cycloalkylalkyl” as used herein, alone or in combination, refers to a carbocycle group attached to a parent molecular moiety through an alkyl group. The term “ester,” as used herein, alone or in combination, refers to a carboxy group bridging two moieties linked at carbon atoms. The term “ether,” as used herein, alone or in combination, refers to an oxy group bridging two moieties linked at carbon atoms.
The term “halo,” or “halogen,” as used herein, alone or in combination, refers to fluorine, chlorine, bromine, or iodine. The term “haloalkoxy,” as used herein, alone or in combination, refers to a haloalkyl group attached to a parent molecular moiety through an oxygen atom. The term “haloalkyl,” as used herein, alone or in combination, refers to an alkyl radical having the meaning as defined above where one or more hydrogens are replaced with a halogen. Specifically included are monohaloalkyl, dihaloalkyl and polyhaloalkyl radicals. A monohaloalkyl radical, for example, sometimes include an iodo, bromo, chloro or fluoro atom within the radical. Dihalo and polyhaloalkyl radicals sometimes include two or more of the same halo atoms or a combination of different halo radicals. Non-limiting examples of haloalkyl radicals include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl. “Haloalkylene” refers to a haloalkyl group attached at two or more positions. Non-limiting examples include fluoromethylene (–CFH–), difluoromethylene (–CF2 –), chloromethylene (–CHCl–) and the like. The term “heteroaliphatic,” as used herein, refers to an aliphatic moiety, as defined herein, that contains one or more heteroatoms, such as, for example, oxygen, nitrogen, sulfur, phosphorous and/or silicon, e.g., in place of a carbon atom or between carbon atoms. In some embodiments, a heteroaliphatic group contains from one to three heteroatoms chosen from O, N, and S, and where the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized. In certain embodiments, the heteroatom(s) may be placed at any interior position of the heteroaliphatic group. In some embodiments, up to two heteroatoms may be consecutive. In certain embodiments, a heteroaliphatic group includes 2 to 20 carbon atoms, 2 to 10 carbon atoms, 2 to 8 carbon atoms or 2 to 6 carbon atoms. The term "heteroalkyl," as used herein, alone or in combination, refers to a saturated or unsaturated, stable straight or branched hydrocarbon chain having the stated number of carbon atoms and one or more heteroatoms, such as, for example, oxygen, nitrogen, sulfur, phosphorous and/or silicon, e.g., in place of a carbon atom. In some embodiments, a heteroalkyl contains from one to three heteroatoms chosen from O, N, and S, and where the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized. In certain embodiments, the heteroatom(s) may be placed at any interior position of the heteroalkyl group. In some embodiments, up to two heteroatoms may be consecutive, such as, for example, -CH2-NH- OCH3. In certain embodiments, a heteroalkyl includes 2 to 20 carbon atoms, 2 to 10 carbon atoms,
2 to 8 carbon atoms or 2 to 6 carbon atoms. In some instances, a heteroalkyl contains from 1 to 3 degrees of unsaturation. Heteroalkyl groups may be optionally substituted as defined herein. The term "heteroaryl," as used herein, alone or in combination, refers to a cyclic ring system in which at least one of the rings is an aromatic ring in which all ring member atoms are carbon, except for at least one heteroatom (referred to herein as a “heteroaryl ring”), such as, for example, nitrogen, oxygen and sulfur. The heteroaryl ring may be optionally substituted as defined herein. A heteroaryl can be a monocyclic or a fused polycyclic, e.g., bicyclic or tricyclic, ring system in which at least one cyclic ring is an aromatic heteroaryl ring. Polycyclic, e.g., bicyclic and tricyclic, fused heteroaryl ring systems as defined herein include heteroaryl ring systems in which one or more heteroaryl rings is/are fused to one or more aryl rings (which are referred to herein as aryl-fused heteroaryl rings), one or more cycloalkyl rings and/or one or more other heteroaryl rings. In some embodiments, all of the rings in a polycyclic heteroaryl ring system are heteroaryl rings. In certain embodiments, a heteroaryl ring contains at least one atom chosen from O, S, and N. In certain embodiments, a heteroaryl ring is a 3 to 15 membered monocyclic ring. In certain embodiments, a monocyclic heteroaryl group may contain from 4 to 10 ring member atoms, and may have, for example, 1 to 4 heteroatoms in the ring, where the remaining ring member atoms are carbon. In some embodiments, a bicyclic heteroaryl ring may contain from 8 to 15 ring member atoms, and have from 1 to 8 heteroatoms, where the remaining ring member atoms are carbon. In some embodiments, a tricyclic heteroaryl ring may contain from 11 to 18 ring member atoms, and have from 1 to 10 heteroatoms, where the remaining ring member atoms are carbon. Non-limiting examples of heteroaryls include pyrrolyl, pyrrolinyl, imidazolyl, pyrazolyl, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, tetrazinyl, triazolyl, tetrazolyl, furyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, thiadiazolyl, isothiazolyl, indolyl, isoindolyl, indolizinyl, benzimidazolyl, quinolyl, isoquinolyl, quinoxalinyl, quinazolinyl, indazolyl, benzotriazolyl, thienopyridinyl, furopyridinyl, pyrrolopyridinyl and the like. Exemplary bicyclic and tricyclic heteroaryl groups include phenanthrolinyl, dibenzofuranyl, acridinyl, phenanthridinyl, dihydro[1,3]oxazolo[4,5-b]pyridinyl, benzothiazolyl, and the like. In polycyclic systems in which a heteroaryl is fused to one or more rings that are not heteroaryl, attachment of the polycycle to the indicated point of attachment on the parent molecule may be through any ring member atom of the polycycle rings. In some embodiments of polycyclic heteroaryls, the polycycle is attached to the indicated point of attachment through a ring member atom of a heteroaryl ring. In some embodiments of monocyclic or polycyclic heteroaryls, the monocyle or polycycle is attached to the indicated point of attachment through a ring member heteroatom of a heteroaryl ring. In some embodiments of polycyclic heteroaryls, the polycycle is attached to the indicated point of attachment through a ring member atom of a ring that is not a heteroaryl ring, e.g., an aryl ring or a cycloalkyl ring. “Heteroaryl”
includes sulfones, sulfoxides, N-oxides of tertiary nitrogen ring member atoms, and carbocyclic fused and benzo-fused ring systems. Non-limiting examples of a heteroaryl group may be referred to as an aryl group having one or more carbon atoms substituted with O, NRn, S, SO, SO2, where “n” denotes any positive integer. The term “heteroarylalkyl” as used herein, alone or in combination, refers to an unsubstituted or substituted heteroaryl group attached to a parent molecular moiety through an alkyl group. The term “lower heteroarylalkyl” as used herein, alone or in combination, refers to an unsubstituted or substituted lower heteroaryl group attached to a parent molecular moiety through a lower alkyl group where "lower heteroaryl" and "lower alkyl" are as defined herein. The term "heteroarylaminoalkyl" as used herein refers to a heteroaryl group attached to a parent molecule through an aminoalkyl group (heteroaryl-N(R)-alkyl-), where R is as defined herein. The term "lower heteroarylaminoalkyl" as used herein refers to a lower heteroaryl group attached to a parent molecule through a lower aminoalkyl group (lower heteroaryl-N(R)-lower alkyl-), where "lower heteroaryl," "lower alkyl" and R are as defined herein. The term “heterocycle-alkyl” as used herein, alone or in combination, refers to a substituted or unsubstituted heterocycle group attached to a parent molecular moiety through an alkyl group. The terms “heterocycloalkyl” and, interchangeably, “heterocycle,” or “heterocyclic” as used herein, alone or in combination, each refer to a ring system in which at least one of the rings is a saturated or partially unsaturated, heteroaliphatic, nonaromatic cyclic ring moiety in which all of the ring member atoms are carbon, except for at least one heteroatom (referred to herein as a “heterocycloalkyl ring,” “heterocycle ring” or “heterocyclic ring”). The one or more heteroatoms that can be in the ring include, for example, nitrogen, oxygen, sulfur, phosphorous and/or silicon. In some embodiments, the ring heteroatom or heteroatoms is selected from nitrogen, oxygen and sulfur. The heterocycloalkyl ring may be optionally substituted as defined herein. A heterocycloalkyl is a monocyclic or polycyclic, e.g., bicyclic or tricyclic, ring system in which at least one cyclic ring is a heterocycloalkyl ring. Polycyclic heterocycloalkyl ring systems include fused, bridged and spiro- fused rings. Polycyclic heterocycloalkyl ring systems as defined herein, include ring systems in which one or more heterocycloalkyl rings is/are fused to one or more cycloalkyl, aryl, heteroaryl and/or heterocycloalkyl rings. In some embodiments, all of the rings in a polycyclic heterocycloalkyl ring system are heterocycloalkyl rings. In certain embodiments, a heterocycloalkyl includes 1 to 4 heteroatoms as ring member atoms. In some embodiments, a heterocycloalkyl moiety includes 1 to 2 heteroatoms as ring member atoms. In certain embodiments, a heterocycloalkyl moiety includes 3 to 8 ring member atoms in each ring. In some embodiments, a heterocycloalkyl moiety includes 3 to 7 ring member atoms in each ring. In yet some embodiments, a heterocycloalkyl moiety includes
5 to 6 ring member atoms in each ring. In some embodiments, a heterocycloalkyl can be a 3 to 15 membered nonaromatic ring, or a fused bicyclic, or tricyclic non-aromatic ring, which contains at least one atom chosen from O, S, and N. In certain embodiments, a monocyclic heterocycloalkyl or heterocycle group may contain from 4 to 10 ring member atoms, and may have, for example, 1 to 4 heteroatoms in the ring, where the remaining ring member atoms are carbon. In some embodiments, a bicyclic heterocycloalkyl or heterocycle group may contain from 8 to 15 ring member atoms, and have from 1 to 8 heteroatoms, where the remaining ring member atoms are carbon. In some embodiments, a tricyclic heterocycloalkyl or heterocycle group may contain from 11 to 18 ring member atoms, and have from 1 to 10 heteroatoms, where the remaining ring member atoms are carbon. The term also includes fused polycyclic groups where one or more heterocyclic rings are fused with one or more cycloalkyl rings, aryl, heteroaryl and/or other heterocyclic groups. In polycyclic systems in which a heterocycloalkyl ring is fused to one or more rings that are not heterocycloalkyl, attachment of the polycycle to the indicated point of attachment on the parent molecule may be through any ring member atom of the polycycle rings. In some embodiments of polycyclic heterocycloalkyls, the polycycle is attached to the indicated point of attachment through a ring member atom of a heterocycloalkyl ring. In some embodiments of monocyclic or polycyclic heterocycloalkyls, the monocyle or polycycle is attached to the indicated point of attachment through a ring member heteroatom of a heterocycloalkyl ring. In some embodiments of polycyclic heterocycloalkyls, the polycycle is attached to the indicated point of attachment through a ring member atom of a ring that is not a heterocycloalkyl ring, e.g., an aryl ring, heteroaryl ring or a cycloalkyl ring. “Heterocycloalkyl” and “heterocycle” include sulfones, sulfoxides and N-oxides of tertiary nitrogen ring member atoms. Non-limiting examples of heterocycle groups include aziridinyl, azetidinyl, 1,3-dioxanyl, 1,4-dioxanyl, 1,3-dioxolanyl, morpholinyl, piperazinyl, pyrrolidinyl, piperidinyl, thiomorpholinyl, pyranyl, dihydropyridinyl, tetrahydropyridinyl, carabazolyl, xanthenyl, 1,3-benzodioxolyl, dihydroisoquinolinyl, dihydrocinnolinyl, dihydrobenzodioxinyl, isoindolinyl, dihydroisoindolyl and dihydroindolyl, and the like. The heterocycle groups may be optionally substituted unless specifically prohibited. Non- limiting examples of heterocycloalkyl groups may be referred to as cycloalkyl group having one or more carbon atoms substituted with O, NRn, S, SO, SO2, where n denotes any positive integer. The term “hydroxy,” as used herein, alone or in combination, refers to –OH. The phrase “in the main chain” refers to the longest contiguous or adjacent chain of carbon atoms starting at the point of attachment of a group to the compounds of any one of the formulas disclosed herein. The phrase “linear chain of atoms” refers to the longest straight chain of atoms independently selected from carbon, nitrogen, oxygen and sulfur.
The term “lower,” as used herein, alone or in a combination, where not otherwise specifically defined, means a moiety containing from 1 to and including 6 carbon atoms. A "lower alkyl," for example, refers to an alkyl containing 1 to 6 carbon atoms (C1-C6), 1 to 5 carbon atoms (C1-C5), 1 to 4 carbon atoms (C1-C4), 1 to 3 carbon atoms (C1-C3), or 1 to 2 carbon atoms (C1-C2) (e.g., an alkyl containing 1, 2, 3, 4, 5 or 6 carbon atoms; a C1, C2, C3, C4, C5 or C6 alkyl). The term “lower aryl,” as used herein, alone or in combination, means a C4-C6 aryl group, for example, a C5-C6 aryl group. A lower aryl group sometimes is a C4-C6 aryl ring group, or C5-C6 aryl ring group for example, including without limitation, phenyl. The term may also refer to a C8- C10 bicyclic ring aryl group, for example, including without limitation, napthyl. Lower aryl groups, including phenyl or napthyl, may be optionally substituted as provided. The term “lower heteroaryl,” as used herein, alone or in combination, means a four-membered, five-membered, or six-membered heteroaryl group. A lower heteroaryl group sometimes is (1) a monocyclic heteroaryl ring comprising five or six ring member atoms, of which between one and four of the ring member atoms may be heteroatoms chosen from O, S, and N, or (2) a bicyclic heteroaryl ring, where each of the fused rings comprises five or six ring member atoms, comprising between them one to four heteroatoms chosen from O, S, and N. Lower heteroaryl groups may be optionally substituted as provided. The term “lower cycloalkyl,” as used herein, alone or in combination, means a monocyclic cycloalkyl having between three and six ring member atoms. Non-limiting examples of lower cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Lower cycloalkyl groups may be optionally substituted as provided. The term “lower heterocycloalkyl,” as used herein, alone or in combination, means a monocyclic heterocycloalkyl having between three and six ring member atoms, of which between one and four may be heteroatoms chosen from O, S, and N. Non-limiting examples of lower heterocycloalkyls include pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, and morpholinyl. Lower heterocycloalkyl groups may be optionally substituted as provided. The term “lower amino,” as used herein, alone or in combination, refers to -NRR’, where R and R’ are independently chosen from hydrogen, lower alkyl, and lower heteroalkyl, any of which may be optionally substituted. Additionally, the R and R’ of a lower amino group may combine to form a five- or six-membered heterocycloalkyl, either of which may be optionally substituted. The terms “oxy” or “oxa,” as used herein, alone or in combination, refer to –O–. The term “oxo,” as used herein, alone or in combination, refers to =O.
The term “partially unsaturated,” as used herein, alone or in combination, refers to a straight-chain, branched-chain or ring moiety that includes at least one double or triple bond and that is not fully saturated. The term “partially unsaturated” when used in reference to a ring moiety means a ring having one or multiple sites of unsaturation but does not include aryl rings or heteroaryl rings as defined herein. The term “ring member atoms,” as used herein, refers to all of the atoms that form the covalent structure of a cyclic ring structure. By “saturated” is meant that the carbon-containing group contains no carbon-carbon double or triple bonds. In certain implementations, a composition includes a pharmaceutically acceptable salt of a compound herein. Non-limiting examples of pharmaceutically acceptable salts include carboxylate salts, amino acid addition salts and zwitterionic forms thereof, which are known to those skilled in the art as suitable for use with humans and animals. (See, e.g., Gerge, S. M., et al, "Pharmaceutical Salts," Pharm. Sci. (1977) 66:1-19). In cases where a compound is sufficiently basic or acidic to form a stable nontoxic acid or base salt, a composition includes a pharmaceutically acceptable salt of the compound. Non-limiting examples of pharmaceutically acceptable salts are organic acid addition salts formed with acids that form a physiological acceptable anion, non-limiting examples of which include tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, [alpha]-ketoglutarate, and [alpha]- glycerophosphate. Suitable inorganic salts may also be formed, including hydrochloride, sulfate, nitrate, bicarbonate, and carbonate salts. Pharmaceutically acceptable salts are obtained using standard procedures known in the art. For example, pharmaceutically acceptable salts may be obtained by reacting a sufficiently basic compound with a suitable acid affording a physiologically acceptable anion. Alkali metal (e.g., sodium, potassium or lithium) or alkaline earth metal (e.g., calcium, magnesium) salts of carboxylic acids and other anionic groups in molecules within a pharmaceutical composition also are contemplated. A composition can include an isomer of a compound herein. Non-limiting examples of isomers are stereoisomers (e.g., diastereomers and enantiomers) and structural isomers such as tautomers. A composition can include a mixture containing two or more isomers of a compound herein. In certain instances, a mixture can include an isomer that predominates over one or more other isomers of a compound herein (e.g., the molar amount of one isomer may represent about 55% or more of all isomers of the compound (e.g., about 60% or more, about 65% or more, about 70% or more, about 75% or more, about 80% or more, about 85% or more)). A composition can include an isomerically pure form of a compound herein, in which the molar amount of one isomer can represent about
95% or more (e.g., about 96% or more, about 97% or more, about 98% or more, about 99% or more or about 99.5% or more) of all isomers of the compound. In certain implementations, a compound in a composition provided herein is isolated (e.g., isolated from other types of molecules). A composition containing a compound described herein sometimes is at least about 80% pure, by weight, and sometime is at least about 85% pure, at least about 90% pure, at least about 95% pure, at least about 99% pure, or at least about 99.5% pure. A composition containing a compound described herein that is x% pure, by weight, includes x% by weight of the compound and y% of components other than the compound described, where y% = 100% - x%, by weight. For example, a composition containing a compound described herein that is 90% pure contains 90% by weight of the compound described and 10% by weight of components other than the compound described.
Compositions A composition can contain a compound herein. A compound in a composition can inhibit an activity of a protein kinase (PK; for example, a PK polypeptide). A PK activity can include a PK binding activity (for example, binding of a PK to a substrate that the PK phosphorylates and/or binding of a PK to a binding partner polypeptide that the PK does not phosphorylate) and/or PK catalytic activity (for example, PK substrate phosphorylation activity). In certain instances a compound herein is capable of effectively inhibiting, moderately inhibiting and/or selectively inhibiting a PK activity. A composition containing a compound herein can be for inhibition of a PK activity, inhibition of an activity of two or more PKs, preparation of a medicament and/or for preparation of a treatment of a PK-associated condition. In certain embodiments, a compound in a composition is or has been isolated (for example, isolated from other types of molecules). A compound sometimes is at least about 80% pure, by weight, in a composition and sometime is at least about 85% pure, at least about 90% pure, at least about 95% pure, at least about 99% pure, or at least about 99.5% pure. A compound n that is x% pure, by weight, in a composition includes x% by weight of the compound and y% of components other than the compound, where y% = 100% - x%, by weight. For example, a compound that is 90% pure in a composition contains 90% by weight of the compound and 10% by weight of components other than the compound. A composition containing a compound herein can be a pharmaceutical composition. A pharmaceutical composition can include a compound herein as an active ingredient and one or more pharmaceutically acceptable additives, including one or more pharmaceutically acceptable excipients. One or more pharmaceutically acceptable excipients in a pharmaceutical composition typically form a carrier for the active ingredient. Non-limiting examples of excipient additives include a pharmaceutically acceptable solvent, diluent, isotonic agent, buffering agent, stabilizer, preservative, antioxidant, vasoconstrictive agent, antibacterial agent, antifungal agent, adsorption delaying agent, sustained release agent (for example, for example, U.S. Patent No.5,624,677), and the like. One or more additives can be combined with an active ingredient for the manufacture of a pharmaceutical composition by a method known in the art. A pharmaceutical composition sometimes is prepared as a solid (for example, powder) or liquid (for example, aqueous solution, emulsion (for example, micro-emulsion, nano-emulsion)). Non-limiting examples of solvents and diluents include water, saline, dextrose, ethanol, glycerol, oil, water-miscible organic cosolvents such as acetone or dimethyl sulfoxide (DMSO), and the like. Non-limiting examples of isotonic agents include sodium chloride, dextrose, mannitol, glucose, sucrose, sorbitol, lactose, and the like. Non-limiting examples of buffering agents include
bicarbonate, phosphate, and the like. Phosphate-buffered saline (PBS), which may be buffered to provide a neutral pH, or in certain embodiments an acidic pH, sometimes is utilized. Non-limiting examples of stabilizers include gelatin, albumin, and the like. Non-limiting examples of a preservatives include gentamicin, merthiolate, chlorocresol and the like. Water or saline, when used for preparing a pharmaceutical composition, may be buffered or not buffered. Non-limiting examples of saline solutions that can be used to prepare a pharmaceutical composition include lactated Ringer's solution, acetated Ringer's solution, intravenous sugar solutions (for example, 5% dextrose in normal saline (D5NS), 10% dextrose in normal saline (D10NS), 5% dextrose in half-normal saline (D5HNS) and 10% dextrose in half-normal saline (D10HNS)). Non-limiting example of buffered saline solutions and related solutions include phosphate buffered saline (PBS), TRIS-buffered saline (TBS), Hank's balanced salt solution (HBSS), Earle's balanced salt solution (EBSS), standard saline citrate (SSC), HEPES-buffered saline (HBS), and Gey's balanced salt solution (GBSS). In certain implementations, an additive enhances solubility and/or bioavailability of an active ingredient. A solubility-enhancing additive may include one or more of: a lipid, polyethylene glycol (PEG), polysorbate, glycerol, glycerin, dimethylacetamide, triacetin, an oil (for example, a vegetable oil), or combination thereof. In certain instances, solubility of an active ingredient is characterized by a particular amount of excipient that confers solubility to the active ingredient. Any suitable antioxidant can be included in a pharmaceutical composition, non-limiting examples of which include (1) butylated hydroxytoluene (BHT), (2) butylated hydroxyanisole (BHA), (3) DL- alpha-tocopherol, (4) ascorbyl palmitate and (5) propyl gallate. A pharmaceutical composition can include a mixture of two, three, four or five antioxidants. A concentration of an active ingredient in a liquid composition sometimes is from about 0.1 wt% to about 35 wt%, or sometimes from about 0.5 wt% to about 10 wt%. The concentration in a semi- solid or solid composition such as a gel or a powder sometimes is about 0.1 wt% to about 5 wt%, or sometimes about 0.5 wt% to about 2.5 wt%. Higher concentrations are also appropriate for some solid or semi-solid compositions and may include amounts up to about 25 wt% or up to about 50 wt% or more. A pharmaceutical composition may be prepared according to conventional techniques known in the pharmaceutical industry. In general terms, such techniques include bringing an active ingredient into association with on or more pharmaceutical carrier(s) and/or excipient(s) in liquid form or finely divided solid form, or both, and then shaping the product if required. A pharmaceutical composition may be incorporated into a suitable dosage form (for example, unit dosage form), non-limiting examples of which include a tablet, capsule, gel capsule, liquid syrup,
soft gel, suppository, enema, dressing or device (for example, in a syringe (for example, auto- injection device) or microneedle device). A pharmaceutical composition may be formulated as a suspension in aqueous, non-aqueous, or mixed media. Aqueous suspensions may further contain substances that increase viscosity, including for example, sodium carboxymethylcellulose, sorbitol, and/or dextran. A suspension may also contain one or more stabilizers. An amount of active ingredient required for use in treatment will vary not only with the particular form selected (for example, the salt selected) but also with route of administration, the nature of the condition being treated and the age and condition of the patient and ultimately will be at the discretion of the attendant physician or clinician. Any additive and material used in preparing a unit dosage form typically is pharmaceutically acceptable and substantially non-toxic in the amounts employed. A composition can include a pharmaceutically acceptable ester or amide of a compound herein. In certain implementations, a composition includes a pharmaceutically acceptable salt of a compound herein. Non-limiting examples of pharmaceutically acceptable salts include carboxylate salts, amino acid addition salts and zwitterionic forms thereof, which are known to those skilled in the art as suitable for use with humans and animals. (See, for example, Gerge, S. M., et al, "Pharmaceutical Salts," Pharm. Sci. (1977) 66:1-19). In cases where a compound is sufficiently basic or acidic to form a stable nontoxic acid or base salt, a composition includes a pharmaceutically acceptable salt of the compound. Non-limiting examples of pharmaceutically acceptable salts are organic acid addition salts formed with acids that form a physiological acceptable anion, non-limiting examples of which include tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, [alpha]-ketoglutarate, and [alpha]-glycerophosphate. Suitable inorganic salts may also be formed, including hydrochloride, sulfate, nitrate, bicarbonate, and carbonate salts. Pharmaceutically acceptable salts are obtained using standard procedures known in the art. For example, pharmaceutically acceptable salts may be obtained by reacting a sufficiently basic compound with a suitable acid affording a physiologically acceptable anion. Alkali metal (for example, sodium, potassium or lithium) or alkaline earth metal (for example, calcium, magnesium) salts of carboxylic acids and other anionic groups in molecules within a pharmaceutical composition also are contemplated. A composition can include an isomer of a compound herein. Non-limiting examples of isomers are stereoisomers (e.g., diastereomers and enantiomers) and structural isomers such as tautomers. A composition can include a mixture containing two or more isomers of a compound herein. In certain instances, a mixture can include an isomer that predominates over one or more other isomers of a compound herein (e.g., the molar amount of one isomer may represent about 55% or more of all isomers of the compound (e.g., about 60% or more, about 65% or more, about 70% or more, about 75% or more, about 80% or more, about 85% or more)). A composition can include an isomerically
pure form of a compound herein, in which the molar amount of one isomer can represent about 95% or more (e.g., about 96% or more, about 97% or more, about 98% or more, about 99% or more or about 99.5% or more) of all isomers of the compound. Non-limiting examples of pharmaceutical compositions are provided hereafter. Pharmaceutical composition for oral administration A pharmaceutical composition may be provided as a tablet (for example, ingestible tablet, buccal tablet), troche, capsule (for example, hard- or soft-shell gelatin capsule), drink, elixir, suspension, syrup, wafer, and the like, and/or may be incorporated directly in food or drink that is part of a subject’s diet. Such compositions and preparations sometimes contain at least 0.1% of active ingredient. The percentage of the compositions and preparations may be varied and sometimes are about 2% to about 60% of the weight of a given unit dosage form. The amount of active ingredient in a pharmaceutical composition is such that an effective dosage level can be obtained. Tablets, troches, pills, capsules, and the like may contain one or more of the following: a binder such as gum tragacanth, acacia, corn starch or gelatin; an excipient such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; a sweetening agent such as sucrose, fructose, lactose or aspartame; a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring. When the unit dosage form is a capsule, it may contain, in addition to materials described above, a liquid carrier, such as a vegetable oil or a polyethylene glycol. Various other materials may be present as coatings or to otherwise modify the physical form of the solid unit dosage form. For instance, tablets, pills, or capsules may be coated with gelatin, wax, shellac or sugar and the like. A syrup or elixir may contain the active compound, sucrose or fructose as a sweetening agent, methyl and propylparabens as preservatives, a dye and flavoring such as cherry or orange flavor. Pharmaceutical composition for topical administration For topical administration, a compound herein may be applied in liquid form. A compound herein may be combined with a dermatologically acceptable carrier, which may be a solid or a liquid. A compound herein may be formulated with a solid carrier, which include finely divided solids such as talc, clay, microcrystalline cellulose, silica, alumina and the like. Useful liquid carriers include water, alcohols or glycols or water-alcohol/glycol blends, or phospholipids in propylene glycol/ethylene glycol, in which the a compound herein can be dissolved or dispersed at an effective level, optionally with the aid of non-toxic surfactants. A composition sometimes includes a diluent and sometimes a carrier (for example, assimilable, editable), buffer, preservative and the like. Additives such as fragrances and additional antimicrobial agents can be added to optimize the properties for a given use. A liquid composition can be applied from an absorbent pad, used to impregnate a
bandage or other dressing, or sprayed onto the affected area using a pump-type or aerosol sprayer. A thickener, such as a synthetic polymer, fatty acid, fatty acid salt and/or ester, fatty alcohol, modified cellulose or modified mineral material, can also be employed with a liquid carrier to form a spreadable cream, paste, gel, ointment, soap, and the like, for application directly to the skin of a subject. Pharmaceutical composition for administration by injection A pharmaceutical composition suitable for injection (for example, subcutaneous, intramuscular, intravenous administration) can include a sterile aqueous solution or dispersion or sterile powder for the extemporaneous preparation of a sterile injectable solution or dispersion. An injectable formulation often is sterile and often is fluid. It typically is stable under the conditions of manufacture and storage and typically is preserved against contaminating microorganisms, such as bacteria and fungi. A pharmaceutical composition can be delivered to a subject via any suitable injection device, including without limitation, a syringe, needle or microneedle (for example, including a syringe device for self-administration; auto-injection device). An injectable formulation sometimes includes a carrier, which can be a solvent, excipient, or dispersion medium. A liquid carrier or vehicle can be a solvent or liquid dispersion medium including, for example, water, ethanol, a polyol (for example, glycerol, propylene glycol, liquid polyethylene glycols, and the like), vegetable oil, nontoxic glyceryl ester, or suitable mixture thereof. Fluidity of an injectable formulation can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of a surfactant. Prevention of the action of microorganisms can be affected by an antibacterial and/or antifungal agent, for example, paraben, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In certain instances, an isotonic agent may be included, for example, a sugar or sodium chloride. Prolonged absorption of an injectable composition can be affected by use of an absorption delaying agent, for example, aluminum monostearate and/or gelatin. A pharmaceutical composition may include a co-polymer such as, for example, a co-polymer selected from poly(vinyl alcohol), poly(vinyl pyrrolidone), and hypromellose acetate succinate. A sterile injectable solution can be prepared by incorporating an active ingredient in the required amount in the appropriate solvent with one or more other ingredients, as required, followed by filter sterilization. In the case of a sterile powder for the preparation of a sterile injectable solution, methods of preparation include vacuum drying and freeze-drying techniques, which yield a powder including the active ingredient and any additional desired ingredient present in the previously sterile-filtered solution.
Protein kinase inhibition A compound can be an inhibitor of one or more protein kinases (PKs), and can be used to inhibit one or more PKs. A compound that inhibits a PK can bind to a PK, inhibit PK substrate phosphorylation activity and/or inhibit binding activity of a PK to another entity (for example, a polypeptide to which the PK binds). A compound that is an inhibitor of one or more PKs sometimes is an effective inhibitor, moderate inhibitor, mild inhibitor and/or ineffective inhibitor of one or more PKs. A compound is designated as an “effective inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by greater than 90%; and/or (ii) the compound inhibits PK activity at a measured IC50 value of less than 20 nM. A compound is designated as a “moderate inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by 70% to 90%; and/or (ii) the compound inhibits PK activity at a measured IC50 value between 20 nM and 40 nM. A compound is designated as a “mild inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by 30% to 70%; and/or (ii) the compound inhibits PK activity at a measured IC50 value between 40 nM and 200 nM. A compound is designated as an “ineffective inhibitor” when (i) the compound at a concentration of 100 nM inhibits PK activity by less than 30%; and/or (ii) the compound inhibits PK phosphorylation at a measured IC50 value of greater than 200 nM. An “effective inhibitor” can be used to effectively inhibit a PK, a “moderate inhibitor” can be used to moderately inhibit a PK, a “mild inhibitor” can be used to mildly inhibit a PK, and an “ineffective inhibitor” can be used to ineffectively inhibit or not inhibit a PK. An IC50 value or percent activity can be measured by a suitable assay, such as an in vitro assay that assesses PK phosphorylation activity or PK ligand binding, for example. In certain embodiments, PK inhibition is assessed according to an IC50 value or percent activity measured by a peptide cleavage assay, tracer displacement assay, solid phase inhibitor competition assay, ADP formation assay, as described herein (described in Example 9), for example. In certain embodiments, a compound that contains a quinazolinyl group and an amine-linked phenyl group can be used to inhibit one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. In certain embodiments, a compound that contains a quinazolinyl group and an amine-linked phenyl group can selectively inhibit a JAK2 PK. In certain instances, the compound effectively inhibits or moderately inhibits a JAK2(wt) PK and does not effectively inhibit and does not
moderately inhibit a JAK1(wt) PK (for example, the compound mildly inhibits or ineffectively inhibits a JAK1 PK). In certain instances, the compound inhibits JAK3(wt) PK, and optionally effectively inhibits JAK3(wt) PK, or optionally moderately inhibits a JAK3(wt) PK. In certain instances, the compound inhibits, and optionally effectively inhibits, one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. In certain instances, a compound effectively inhibits two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, SRC family PK, DDR family PK, and/or PTK family PK. In certain instances, the compound moderately inhibits two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. In certain embodiments, a compound that effectively inhibits and/or optionally moderately inhibits a PK in one or more of the foregoing PK families, does not effectively inhibit, and/or does not moderately inhibit, one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. In certain embodiments, a compound used to inhibit a PK is a compound herein (in Table A, for example). In certain instances, a composition used to inhibit a PK contains a compound herein (in Table A, for example). A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an ABL family PK, including an ABL1 PK, including ABL1(wt) and/or one or more ABL1 variants; and/or an ABL2 PK, including ABL2(wt) and/or one or more ABL2 variants. An ABL1 variant can include one or more of the following amino acid substitutions (relative to ABL1(wt)): T315I, G250E,
Q252H, Y253F, E255K, F317L, M351T and H396P, and/or other ABL1 amino acid substitution described herein. An ABL2 PK also is referred to as an ARG PK. A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a BTK family PK. A BTK family PK can include: a BTK PK, including BTK(wt) and/or one or more BTK variants; a BMX PK, including BMX(wt) and/or one or more BMX variants; an ITK PK, including ITK(wt) and/or one or more ITK variants; a TEC PK, including TEC(wt) and/or one or more TEC variants; and a TXK PK, including TXK(wt) and/or one or more TXK variants. BMX is referred to also as ETK, ITK is referred to also as EMT and TXK is referred to also as RLK. A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an Aurora (AURK) family PK. An AURK family PK can include: an AURKA PK, including AURKA(wt) and/or one or more AURKA variants; an AURKB PK, including AURKB(wt) and/or one or more AURKB variants; and an AURKC PK, including AURKC(wt) and/or one or more AURKC variants. A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a JAK family PK. A JAK family PK can include: a JAK1 PK, including JAK1(wt) and/or one or more JAK1 variants; a JAK2 PK, including JAK2(wt) and/or one or more JAK2 variants; a JAK3 PK including JAK3(wt) and/or one or more JAK3 variants; and a TYK family PK. A TYK family PK can be a TYK2 family PK, including TYK2(wt) and/or one or more TYK2 variants. A JAK2 PK variant can include the amino acid substitution V617F, relative to JAK2(wt). A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a TYK2 family PK and sometimes is a Subgroup 2 compound. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a TRK family PK. A TRK family PK can include: a TRKA PK, including TRKA(wt) and/or one or more TRKA variants; a TRKB PK, including TRKB(wt) and/or one or more TRKB variants; a TRKC PK, including TRKC(wt) and/or one or more TRKC variants; and a ROS1 PK, including ROS1(wt) and/or one or more ROS1 variants. TRKA is referred to also as NTRK1, TRKB is referred to also as NTRK2, and TRKC is referred to also as NTRK3. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an EPH family PK. An EPH family PK can include an EPHA1 PK, including EPHA1(wt) and/or one or more EPHA1 variants; an EPHA2 PK, including EPHA2(wt) and/or one or more EPHA2 variants; an EPHA5 PK, including EPHA5(wt) and/or one or more EPHA5 variants; an EPHA8 PK, including EPHA8(wt) and/or one or more EPHA8 variants; an EPHB1 PK, including EPHB1(wt) and/or one or more EPHB1 variants; and/or an EPHB2 PK, including EPHB2(wt) and/or one or more EPHB2 variants.
A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a TNK family PK. A TNK family PK can include a TNK1 PK, including TNK1(wt) and/or one or more TNK1 variants; and/or a TNK2 PK, including TNK2(wt) and/or one or more TNK2 variants. A TNK2 PK sometimes is referred to as an ACK PK. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a PTK family PK. A PTK family PK can include a PTK2B PK, including PTK2B(wt) and/or one or more PTK2B variants. A PTK2B PK can be referred to as a FAK2 PK. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a SRC family PK. A SRC family PK can include a SRC(wt) and/or one or more SRC variants, and a SRC-N1(wt) and/or one or more SRC-N1 variants. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a LCK family PK. A LCK family PK can include a LCK(wt) and/or one or more LCK variants. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a DDR family PK. A DDR family PK can include a DDR2 PK, including DDR2(wt) and/or one or more DDR2 variants. A DDR variant PK can include a T654M and/or N456S amino acid substitution. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a PLK family PK. A PLK family PK can include PLK4(wt) and/or one or more PLK4 variants. A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a PLK4 family PK and sometimes is a Subgroup 3 compound. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, an IRAK family PK. An IRAK family PK can include an IRAK1 PK, including IRAK1(wt) and/or one or more IRAK1 variants; and/or an IRAK3 PK, including IRAK3(wt) and/or one or more IRAK3 variants. A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a RET family PK. A RET family PK can include: a RET PK, including RET(wt) and/or one or more RET variants. A RET variant can include one or more of the following amino acid substitutions, relative to RET(wt): A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F. A compound that inhibits a RET family PK sometimes also inhibits BMX, BTK, TXK, JAK1, JAK2, JAK3, TRKA, TRKB, TRKC, AURKA, an EPH family PK, IRAK3 and PLK4. A compound can be an effective inhibitor or moderate inhibitor of, and can be used to inhibit, a RET family PK and the compound sometimes is a Subgroup 2 compound.
A compound sometimes is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, one or more, or two or more, variants of a PK. In certain embodiments, a compound is an effective inhibitor or moderate inhibitor of, and can be used to inhibit, one or more of the following PK variants: (i) an ABL1 variant optionally containing one or more of the following amino acid substitutions relative to ABL1(wt): T315I, G250E, Q252H, Y253F, E255K, F317L, M351T and H396P; (ii) a JAK2 PK variant optionally containing the amino acid substitution V617F relative to JAK2(wt); (iii) a RET variant optionally containing one or more of the following amino acid substitutions relative to RET(wt): A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F; and/or (iv) a DDR2 variant optionally containing the amino acid substitution T654M relative to DDR2(wt) and/or the amino acid substitution N456S relative to DDR2(wt). A PK variant can be referred to with the PK name as a prefix and an amino acid substation as a suffix, where the amino acid substation suffix is separated from the PK name prefix by a hyphen (for example, ABL1-T315I or DDR2-N456S) or by parentheses (for example, ABL1(T315I) or DDR2(N456S)). A compound can be an effective inhibitor of, and can be used to inhibit, two or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. A compound can be an effective inhibitor of, and can be used to inhibit, an ABL family PK and a BTK family PK (for example, a BTK(wt) PK). A compound can be an effective inhibitor of, and can be used to inhibit, an ABL family PK and a AURK family PK. A compound can be an effective inhibitor of, and can be used to inhibit, an ABL family PK and a JAK family PK (for example, JAK2(wt) and/or JAK2(V617F)). A compound can be an effective inhibitor of, and can be used to inhibit, three or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. A compound can be an effective inhibitor of an ABL family PK (for example, ABL1(wt) and/or ABL1(T315I)), a BTK family PK (for example, a BTK(wt) PK) and a AURK family PK, for example. A compound can be an effective inhibitor of, and can be used to inhibit, four or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. A compound can be an effective inhibitor of: an ABL family PK (for example, ABL1(wt) and/or ABL1(T315I)), a BTK family PK (for example, a BTK(wt) PK), a AURK family PK, and a JAK family PK. A compound can be an effective inhibitor of: an ABL family PK (for example, ABL1(wt) and/or ABL1(T315I)), a BTK family PK (for example, a
BTK(wt) PK), a AURK family PK, a JAK family PK (for example, JAK2(wt) PK and/or JAK2 variant PK containing a V617F amino acid substitution), and a TRK family PK. A compound can be an effective inhibitor of, and can be used to inhibit, five of, or six of, or seven of, or eight of, or nine of, or ten of, or eleven of, or twelve of, or thirteen of or all of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK, and can be a Subgroup 1 compound. A compound of Subgroup 1 can be an effective inhibitor of, or optionally a moderate inhibitor of, and can be used to inhibit, multiple PTKs, including ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or all of an ABL family PK, a BTK family PK, an AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a DDR family PK, and/or a PTK family PK. A compound can inhibit a homo sapiens PK or viral PK. A polypeptide of each of the foregoing wild type (wt) homo sapiens PKs is accessible in (i) a public database (World Wide Web URL ncbi.nlm.nih.gov/protein/) according to the corresponding accession number having a “NP” or “AA” prefix, and (ii) a public database (World Wide Web URL uniprot.org/uniprotkb/) according to the corresponding accession number having a “P” prefix, in Table 4 of Example 9. A polypeptide of a corresponding PK variant can be determined according to the wt polypeptide accessed from the database and the position of one or more amino acid substitutions designated. JAK1(wt), JAK2(wt) and JAK3(wt) are receptor PKs. The JAK1(wt) catalytic domain includes amino acids 866-1154 of the JAK1(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The JAK2(wt) catalytic domain includes amino acids 808-1132 of the JAK2(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The JAK3(wt) catalytic domain includes amino acids 781-1124 of the JAK3(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. TRKA(wt), TRKB(wt) and TRKC(wt) also are receptor PKs. The TRKA(wt) catalytic domain includes amino acids 441-796 of the TRKA(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The TRKB(wt) catalytic domain includes amino acids 526-838 of the TRKB(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The TRKC(wt) catalytic domain includes amino acids 510-825 of the TRKC(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. RET(wt) also is a receptor PK and the catalytic domain includes
amino acids 658-1114 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. EPHA1(wt), EPHA2(wt), EPHA5(wt), EPHA8(wt), EPHB1(wt) and EPHB2(wt) PKs also are receptor PKs. The EPHA1(wt) catalytic domain includes amino acids 568-976 of the EPHA1(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The EPHA2(wt) catalytic domain includes amino acids 560-976 of the EPHA2(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The EPHA5(wt) catalytic domain includes amino acids 595-1037 of the EPHA5(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The EPHA8(wt) catalytic domain includes amino acids 565-1005 of the EPHA8(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The EPHB1(wt) catalytic domain includes amino acids 612-887 of the EPHB1(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The EPHB2(wt) catalytic domain includes amino acids 616-884 of the EPHB2(wt) polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. TYK2(wt) also is a receptor PK and the catalytic domain includes amino acids 833-1187 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. TNK2(wt), which also is referred to as ACK, also is a receptor PK and the catalytic domain includes amino acids 110-476 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. IRAK1(wt) also is a receptor PK and the catalytic domain includes amino acids 194-712 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. DDR2 also is a receptor PK and the catalytic domain includes amino acids 422-855 of the polypeptide accessed by the accession number in Table 4 of Example 9, which can be utilized in assays. The SRC(wt) polypeptide can be accessed by either of the accession numbers shown in Table 4 of Example 9. The SRC-N1(wt) polypeptide is nearly identical to the SRC(wt) polypeptide but includes a 6-amino acid polypeptide insertion in the SH3 domain of the SRC(wt) polypeptide. The T at position 117 in the SRC(wt) polypeptide is replaced by TRKVDVR in the SRC-N1(wt) polypeptide. A PK referred to herein as ABL1, ABL2, AURKA, AURKB, AURK3, BTK, BMX, ITK, TEC, TXK, JAK1, JAK2, JAK3, TYK2, ROS1, EPHA1, EPHA2, EPHA5, EPHA8, EPHB1, EPHB2, IRAK1, IRAK3, PLK4, TNK1, TNK2, RET, TRKA, TRKB, TRKC, NTRK1, NTRK2, NTRK3, SRC, SRC-N1, LCK, DDR2 or PTK2B, without an indication of an amino acid substitution, typically contains the polypeptide of ABL1(wt), ABL2(wt), AURKA(wt), AURKB(wt), AURK3(wt), BTK(wt), BMX(wt),
ITK(wt), TEC(wt), TXK(wt), JAK1(wt), JAK2(wt), JAK3(wt), TYK2(wt), ROS1(wt), EPHA1(wt), EPHA2(wt), EPHA5(wt), EPHA8(wt), EPHB1(wt), EPHB2(wt), IRAK1(wt), IRAK3(wt), PLK4(wt), TNK1(wt), TNK2(wt), RET(wt), TRKA(wt), TRKB(wt), TRKC(wt), NTRK1(wt), NTRK2(wt), NTRK3(wt), SRC(wt), SRC-N1(wt), LCK(wt), DDR2(wt) or PTK2B(wt), respectively, or a portion thereof containing (i) a catalytic domain or (ii) a fragment of a catalytic domain having phosphoryl- transfer activity (for example, in vitro phosphoryl-transfer activity). A PK referred to as having an amino acid substitution herein (for example DDR2-N456S and/or DDR2-T654M) typically includes the designated amino acid substitution at the designated position in the polypeptide accessed by the accession number referenced in Table 4 of Example 9, and can be the length of the accessed polypeptide, or a portion thereof containing (i) a catalytic domain or (ii) a fragment of a catalytic domain having phosphoryl-transfer activity (for example, in vitro phosphoryl-transfer activity). ABL1 inhibition In certain embodiments, a compound is an effective inhibitor or moderate inhibitor of one or more, or two or more, ABL1 variant polypeptides. Such a compound can be an effective inhibitor or moderate inhibitor of ABL1(wt). A compound that is an effective inhibitor or two or more ABL1 variant polypeptides can be considered a pan-ABL1 inhibitor. In certain embodiments, a compound is an effective inhibitor of two or more ABL1 variant polypeptides containing one or more of M244V, G250E, Q252H, Y253F, Y253H, E255K, E255V, V299L, F311L, T315A, T315I, F317L, F317V, M351T, E355G, F359V, V379I, L387M, H396P and/or H396R. A compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of one or more other ABL1 variant polypeptides (for example, two or more other ABL1 variant polypeptides, three or more other ABL1 variant polypeptides, or four or more other ABL1 variant polypeptides). A compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of one or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L). A compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of two or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L). A compound sometimes is an effective inhibitor of ABL1(T315I) and an effective inhibitor of three or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L). A compound sometimes is an effective inhibitor of ABL1(T315I), an effective inhibitor one or more other ABL1 variant polypeptides, and a moderate inhibitor of one or more other ABL1 variant polypeptides. A compound sometimes is an effective inhibitor of ABL1(T315I), an effective inhibitor of one or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L), and a moderate inhibitor of one or more of ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L). A compound sometimes is an effective inhibitor of ABL1(T315I), ABL1(G250E), ABL1(Y253F) and ABL1(E255K), and a moderate inhibitor of ABL1(F317L).
ABL1(wt) and ABL1 variant polypeptides are described in greater detail hereafter. Two common alternatively spliced isoforms of the homo sapiens ABL1 PTK are referred to herein as "isoform a" and "isoform b." The following is the ABL1 "isoform a" polypeptide (SEQ ID NO:1). MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPN LFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWY HGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRF NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEV YEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTY GNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGL SRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQV YELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGK QGVRGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDHEPAVSPLLPRKE
LWKKSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDS an
underlined with double-underlining, followed by a catalytic domain highlighted in bold text, followed by a C-terminal region underlined with hatched underlining. The ABL1 "isoform a" polypeptide N- terminal region underlined above by single underlining differs from the ABL1 "isoform b" polypeptide N-terminal region underlined above by single underlining. The adjacent, downstream polypeptide region in each of the ABL1 "isoform a" polypeptide and ABL1 "isoform b" polypeptide, which is not underlined with single underlining, and which starts from the end of the N-terminal region underlined by single underlining and ends at the C-terminus, is identical (the "identical portion"). The common catalytic domain (also referred to as a "kinase domain") highlighted in bold text in the ABL1 "isoform a" polypeptide and ABL1 "isoform b" polypeptide above is reproduced below (SEQ ID NO:3). SPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKE
NO:3) is addressed hereafter. An ABL1 polypeptide referred to as an "ABL1 wild type" polypeptide ("ABL1(wt)") can (1) contain the polypeptide of SEQ ID NO:3; or (2) contain the polypeptide of SEQ ID NO:1; or (3) contain the polypeptide of SEQ ID NO:2; or (4) contain the polypeptide of SEQ ID NO:3 and: (i) an adjacent N- terminal region containing 2 or more contiguous amino acids in the double-underlined region and/or single underlined region shown above in SEQ ID NO:1 or SEQ ID NO:2, or (ii) an adjacent C- terminal region containing 2 or more contiguous amino acids in the hatched-underlined region shown above in SEQ ID NO:1 and SEQ ID NO:2, or a combination of (i) and (ii); or (5) contain a
fragment of (1), (2), (3) or (4) containing 25 or more contiguous amino acids or 1100 or fewer contiguous amino acids; or (6) contain an ABL1 polypeptide portion containing a polypeptide of (1), (2), (3), (4) or (5) and a non-ABL1 polypeptide portion. An ABL1(wt) polypeptide typically does not include a substitution of an amino acid in the identical portion, i.e., the portion of the ABL1 "isoform a" and "isoform b" polypeptides above not underlined by single-underlining. An ABL1(wt) polypeptide typically includes no amino acid insertion or amino acid deletion relative to the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3. A fragment sometimes includes 25 or more contiguous amino acids of the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 (for example, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 65 or more, 70 or more, 75 or more, 80 or more, 85 or more, 90 or more, 95 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more, 160 or more, 170 or more, 180 or more, 190 or more, 200 or more, 225 or more, 250 or more, 275 or more, 300 or more, 325 or more, 350 or more, 375 or more, 400 or more, 425 or more, 450 or more, 475 or more, 500 or more, 525 or more, 550 or more, 575 or more, 600 or more, 625 or more, 650 or more, 675 or more, 700 or more, 725 or more, 750 or more, 775 or more, 800 or more, 825 or more, 850 or more, 875 or more, 900 or more, 925 or more, 950 or more, 975 or more, 1000 or more, 1025 or more, 1050 or more, 1075 or more, or 1100 or more contiguous amino acids of the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3). A fragment sometimes includes 1100 or fewer contiguous amino acids of the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 (for example, 50 or fewer, 55 or fewer, 60 or fewer, 65 or fewer, 70 or fewer, 75 or fewer, 80 or fewer, 85 or fewer, 90 or fewer, 95 or fewer, 100 or fewer, 110 or fewer, 120 or fewer, 130 or fewer, 140 or fewer, 150 or fewer, 160 or fewer, 170 or fewer, 180 or fewer, 190 or fewer, 200 or fewer, 225 or fewer, 250 or fewer, 275 or fewer, 300 or fewer, 325 or fewer, 350 or fewer, 375 or fewer, 400 or fewer, 425 or fewer, 450 or fewer, 475 or fewer, 500 or fewer, 525 or fewer, 550 or fewer, 575 or fewer, 600 or fewer, 625 or fewer, 650 or fewer, 675 or fewer, 700 or fewer, 725 or fewer, 750 or fewer, 775 or fewer, 800 or fewer, 825 or fewer, 850 or fewer, 875 or fewer, 900 or fewer, 925 or fewer, 950 or fewer, 975 or fewer, 1000 or fewer, 1025 or fewer, 1050 or fewer, or 1075 or fewer contiguous amino acids of the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3). A non-ABL1 polypeptide portion present in an ABL1(wt) polypeptide sometime is (i) an N-terminal portion, or is located closer to the N-terminus of the ABL1(wt) polypeptide than the ABL1 polypeptide portion; or (ii) a C-terminal portion, or is located closer to the C-terminus of the ABL1(wt) polypeptide than the ABL1 polypeptide portion; or (iii) a combination of (i) and (ii) where there are multiple non-ABL1 polypeptide portions. A non-ABL1 polypeptide portion present in an ABL1(wt) polypeptide sometimes contains a BCR portion (for example, a BCR portion of a BCR-
ABL1 fusion polypeptide identified in cancer patients). A BCR portion present in an ABL1(wt) polypeptide can be an N-terminal portion, or can be located closer to the N-terminus of the ABL1(wt) polypeptide than the ABL1 polypeptide portion. An ABL1(wt) polypeptide can be modified with one or more components that facilitate use of the polypeptide, including without limitation one or more of separating, purifying, isolating and detecting an ABL1 polypeptide, and measuring an activity of an ABL1 polypeptide (for example, binding activity of an ABL1 polypeptide to a test compound and/or binding agent; phosphorylation activity of an ABL1 polypeptide). In certain embodiments, an ABL1(wt) polypeptide can be modified to include a binding pair member (for example, biotin/avidin (or streptavidin), antibody/antigen), a luminescence molecule (for example, bioluminescence molecule; luciferase or portion thereof; nano-luciferase), fluorophore (for example, member or members of a fluorescence resonance energy transfer (FRET) pair), dye, particle (for example, nanoparticle), and the like, for example. For embodiments in which the component is a polypeptide, the polypeptide may be a non-ABL polypeptide portion referenced herein. In certain instances, a non-ABL1 polypeptide portion is an N-terminal or C-terminal portion useful to immobilizing the ABL1 polypeptide to a solid phase. In certain embodiments, a non-ABL polypeptide portion contains a poly-histidine peptide portion (for example, a peptide containing 5-20, or 6-10, consecutive histidine amino acids) capable of associating with a transition metal-containing solid phase (for example, a solid phase containing Mn, Fe, Co, Ni or Cu). A non-ABL1 polypeptide portion sometimes contains one or both of a linker polypeptide portion and a cleavage recognition polypeptide portion. Multiple linker polypeptide portions are known and can be selected. Multiple cleavage recognition polypeptide portions also are known and can be selected for cleavage of an N-terminal portion or C-terminal portion from an ABL1 polypeptide under suitable cleavage conditions. A non-limiting example of an ABL1(wt) polypeptide containing the "isoform a" polypeptide of SEQ ID NO:1 and a non-ABL1 C-terminal portion (highlighted in bold text) containing a poly-histidine peptide portion and linker portion, referred to herein as "isoahABL1(wt)," is as follows (SEQ ID NO:4): MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPN LFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWY HGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRF NTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEV YEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTY GNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGL SRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQV
YELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGK QGVRGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESDPLDHEPAVSPLLPRKE RGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSSFREMDGQPERRGAGEEEGRD ISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSPHLWKKSSTLTSSRLATGEEE GGGSSSKRFLRSCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTFGGHKSEKPALPRKRAG ENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPKPLRRQVTVAPASGLPH KEEAGKGSALGTPAAAEPVTPTSKAGSGAPGGTSKGPAEESRVRRHKHSSESPGRDKGKLSRLK PAPPPPPAASAGKAGGKPSQSPSQEAAGEAVLGAKTKATSLVDAVNSDAAKPSQPGEGLKKPVL PATPKPQSAKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLISTRVSLRKTRQPPERIAS GAITKGVVLDSTEALCLAISRNSEQMASHSAVLEAGKNLYTFCVSYVDSIQQMRNKFAFREAIN KLENNLRELQICPATAGSGPAATQDFSKLLSSVKEISDIVQRLEACQLGTDDYDIPTTHHHHHH A non-limiting example of an ABL1(wt) polypeptide containing the "isoform b" polypeptide of SEQ ID NO:2 and a non-ABL1 N-terminal portion (highlighted in bold text) containing a nano-luciferase portion and linker portion, referred to herein as "isoblABL1(wt)," is as follows (SEQ ID NO:5): MVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSGENGLKIDIHVIIPY EGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGTLVIDGVTPNMIDYFGRPYEGIAVFDGKKIT VTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERILAGGSGGGGSGGGSSGGAIAMGQ QPGKVLGDQRRPSLPALHFIKGAGKKESSRHGGPHCNVFVEHEALQRPVASDFEPQGLSEAARW NSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVP SNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRI NTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERT DITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGV CTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARN CLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEI ATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETM FQESSISDEVEKELGKQGVRGAVSTLLQAPELPTKTRTSRRAAEHRDTTDVPEMPHSKGQGESD PLDHEPAVSPLLPRKERGPPEGGLNEDERLLPKDKKTNLFSALIKKKKKTAPTPPKRSSSFREM DGQPERRGAGEEEGRDISNGALAFTPLDTADPAKSPKPSNGAGVPNGALRESGGSGFRSPHLWK KSSTLTSSRLATGEEEGGGSSSKRFLRSCSASCVPHGAKDTEWRSVTLPRDLQSTGRQFDSSTF GGHKSEKPALPRKRAGENRSDQVTRGTVTPPPRLVKKNEEAADEVFKDIMESSPGSSPPNLTPK PLRRQVTVAPASGLPHKEEAGKGSALGTPAAAEPVTPTSKAGSGAPGGTSKGPAEESRVRRHKH SSESPGRDKGKLSRLKPAPPPPPAASAGKAGGKPSQSPSQEAAGEAVLGAKTKATSLVDAVNSD AAKPSQPGEGLKKPVLPATPKPQSAKPSGTPISPAPVPSTLPSASSALAGDQPSSTAFIPLIST
RVSLRKTRQPPERIASGAITKGVVLDSTEALCLAISRNSEQMASHSAVLEAGKNLYTFCVSYVD SIQQMRNKFAFREAINKLENNLRELQICPATAGSGPAATQDFSKLLSSVKEISDIVQR The "isoahABL1(wt)" polypeptide can be utilized in a labeled peptide cleavage assay (for example, assay described in Example 9). The "isoblABL1(wt)" polypeptide can be utilized in a labeled peptide competition assay, such as a bioluminescence resonance energy transfer (BRET) intracellular assay (for example, Machleidt et al., ACS Chem. Biol.10:1797-1804 (2015)), for example. An ABL1 polypeptide referred to herein as an "ABL1 variant polypeptide" typically includes one or more amino acid substitutions relative to an ABL1(wt) polypeptide. An ABL1 variant polypeptide may include a structure described herein for an ABL1(wt) polypeptide, with the exception that the variant polypeptide includes one or more amino acid substitutions relative to the ABL1(wt) polypeptide. An ABL1 variant polypeptide sometimes includes up to ten amino acid substitutions relative to an ABL1(wt) polypeptide (for example, substitution of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids relative to an ABL1(wt) polypeptide). An amino acid substitution in an ABL1 variant polypeptide is defined herein relative to a position in SEQ ID NO:1, by the following notation utilizing the one-letter amino acid code: amino acid in SEQ ID NO:1 - at position in SEQ ID NO:1 - corresponding substituted amino acid in ABL1 variant polypeptide. For example, the amino acid substitution notated as "T315I" refers to the threonine at position 315 in SEQ ID NO:1 substituted by isoleucine in an ABL1 variant ("ABL1(T315I)"). An ABL1 variant polypeptide can include an amino acid substitution corresponding to a position in SEQ ID NO:1 in instances where the ABL1 variant polypeptide includes the same number, or does not include the same number, of amino acids of the polypeptide of SEQ ID NO:1. A corresponding amino acid position of an amino acid substitution can be readily determined for a particular ABL1 variant polypeptide as known in the art. A corresponding amino acid position in an ABL1 variant polypeptide can be determined by aligning the ABL1 variant polypeptide to the polypeptide of SEQ ID NO:1, as known in the art, and determining the position of the substituted amino acid in the ABL1 variant polypeptide corresponding to the amino acid position of SEQ ID NO:1 in the alignment (for example, World Wide Web Uniform Resource Locator (URL) Hypertext Transfer Protocol Secure: blast.ncbi.nlm.nih.gov/ Blast.cgi?PAGE=Proteins). For example, the threonine highlighted in bold text and underlined in the catalytic domain polypeptide shown herein (SEQ ID NO:3) corresponds to threonine 315 in SEQ ID NO:1. An ABL1 variant polypeptide often includes no amino acid insertion or amino acid deletion relative to the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3. An ABL1 variant polypeptide
can, in certain instances, include (i) an amino acid insertion within the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 containing 1, 2 or 3 contiguous amino acids; or (ii) an amino acid deletion of 1, 2 or 3 contiguous amino acids in the polypeptide of SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3; or a combination of (i) and (ii). An ABL1 variant polypeptide may include an amino acid substitution in a particular portion of the polypeptide, non-limiting examples of which include a p-loop portion, SH3 contact portion, SH2 contact portion and A-loop portion. Non-limiting examples of amino acid substitutions, any one or more of which may be present in an ABL1 variant polypeptide, are illustrated in FIG.2 (Soverini et al., Blood 118(5):1208-1215 (2011)). An ABL1 variant may include one or more of the following amino acid substitutions: M237V, I242T, M244V, K247R, L248V, G250E, G250R, Q252R, Q252H, Y253F, Y253H, E255K, E255V, E258D, W261L, L273M, E275K, E275Q, D276G, T277A, E279K, V280A, V289A, V289I, E292V, E292Q, I293V, L298V, V299L, F311L, F311I, T315A, T315I, F317L, F317V, F317I, F317C, Y320C, L324Q, Y342H, M343T, A344V, A350V, M351T, E355D, E355G, E355A, F359V, F359I, F359C, F359L, D363Y, L364I, A365V, A366G, L370P, V371A, E373K, V379I, A380T, F382L, L384M, L387M, L387F, L387V, M388L, Y393C, H396P, H396R, H396A, A397P, S417F, S417Y, I418S, I418V, A433T, S438C, E450K, E450G, E450A, E450V, E453G, E453K, E453V, E453Q, E459K, E459V, E459G, E459Q, M472I, P480L, F486S and E507G. The foregoing amino acid substitutions have been reported to confer imatinib therapy resistance in CML patients. Substitutions F317L and V299L have been reported to impart dasatinib therapy resistance and substitutions Y253H, E255K, E255V, F359V and F359C have been reported to impart nilotinib therapy resistance. The substitution T315I has been reported to impart resistance to imatinib, dasatinib and nilotinib therapy. Non-limiting examples of ABL1 variant polypeptides are referred to herein as ABL1(M237V), ABL1(I242T), ABL1(M244V), ABL1(K247R), ABL1(L248V), ABL1(G250E), ABL1(G250R), ABL1(Q252R), ABL1(Q252H), ABL1(Y253F), ABL1(Y253H), ABL1(E255K), ABL1(E255V), ABL1(E258D), ABL1(W261L), ABL1(L273M), ABL1(E275K), ABL1(E275Q), ABL1(D276G), ABL1(T277A), ABL1(E279K), ABL1(V280A), ABL1(V289A), ABL1(V289I), ABL1(E292V), ABL1(E292Q), ABL1(I293V), ABL1(L298V), ABL1(V299L), ABL1(F311L), ABL1(F311I), ABL1(T315A), ABL1(T315I), ABL1(F317L), ABL1(F317V), ABL1(F317I), ABL1(F317C), ABL1(Y320C), ABL1(L324Q), ABL1(Y342H), ABL1(M343T), ABL1(A344V), ABL1(A350V), ABL1(M351T), ABL1(E355D), ABL1(E355G), ABL1(E355A), ABL1(F359V), ABL1(F359I), ABL1(F359C), ABL1(F359L), ABL1(D363Y), ABL1(L364I), ABL1(A365V), ABL1(A366G), ABL1(L370P), ABL1(V371A), ABL1(E373K), ABL1(V379I), ABL1(A380T), ABL1(F382L), ABL1(L384M), ABL1(L387M), ABL1(L387F), ABL1(L387V), ABL1(M388L), ABL1(Y393C), ABL1(H396P), ABL1(H396R), ABL1(H396A), ABL1(A397P), ABL1(S417F), ABL1(S417Y),
ABL1(I418S), ABL1(I418V), ABL1(A433T), ABL1(S438C), ABL1(E450K), ABL1(E450G), ABL1(E450A), ABL1(E450V), ABL1(E453G), ABL1(E453K), ABL1(E453V), ABL1(E453Q), ABL1(E459K), ABL1(E459V), ABL1(E459G), ABL1(E459Q), ABL1(M472I), ABL1(P480L), ABL1(F486S) or ABL1(E507G). A non-limiting example of an ABL1 variant polypeptide contains the polypeptide of SEQ ID NO:3 with one or more of the following modifications: (i) the threonine highlighted in bold text and underlined in the polypeptide of SEQ ID NO:3 herein is substituted to isoleucine, (ii) a polyhistidine tag containing ten consecutive histidine amino acids is appended at the N-terminus along with an adjacent 3’ linker sequence (SSGVDLGT) followed by a “TEV” cleavage site (ENLYFQ/S), and (iii) an initial “MG” sequence. An example of an ABL1 variant polypeptide containing the foregoing modifications is referred to as "catABL1(T315I)" herein and contains the following polypeptide (SEQ ID NO:6). MGHHHHHHHHHHSSGVDLGTENLYFQ/SSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKY SLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIIIEFMTYGNLLDYLR ECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDT YTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDY RMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGK In the polypeptide of SEQ ID NO:6 depicted above, the forward slash designates the TEV cleavage site and does not designate an amino acid (i.e., the Q and S immediately flanking the forward slash are contiguous). An ABL1 variant polypeptide can have the same or about the same substrate phosphorylation activity of an ABL1(wt) polypeptide containing the polypeptide of SEQ ID NO:1 under phosphorylation conditions, when the polypeptide is not contacted by a test compound. An ABL1 variant polypeptide can have a substrate phosphorylation activity lower than the phosphorylation activity of an ABL1(wt) polypeptide containing the polypeptide of SEQ ID NO:1 under phosphorylation conditions, when the polypeptide is not contacted by a test compound (for example, a substrate phosphorylation activity within about 10-fold, or 9-fold, or 8-fold, or 7-fold, or 6-fold, or 5-fold, or 4-fold, or 3-fold, or 2-fold, lower than the substrate phosphorylation activity of the ABL1(wt) polypeptide). An ABL1 variant polypeptide can have a substrate phosphorylation activity greater than the phosphorylation activity of an ABL1(wt) polypeptide containing the polypeptide of SEQ ID NO:1 under phosphorylation conditions, when the polypeptide is not contacted by a test compound (for example, a substrate phosphorylation activity within about 10- fold, or 9-fold, or 8-fold, or 7-fold, or 6-fold, or 5-fold, or 4-fold, or 3-fold, or 2-fold, greater than the substrate phosphorylation activity of the ABL1(wt) polypeptide). Phosphorylation activity of an ABL1
variant polypeptide can be determined by a suitable assay, which can be an in vitro assay (for example, a labeled peptide cleavage assay described herein), for example. Protein kinase inhibitor assessment A compound herein can inhibit a protein kinase (PK) activity. A compound can be assessed as a test compound in a suitable assay or system to determine PK inhibitor activity. A test compound assessed by an assay for PK inhibitor activity sometimes is a compound herein and/or sometimes is another compound, such as a clinically approved PK inhibitor, for example. An assay sometimes is conducted in vitro or in vivo. An in vitro assay sometimes quantifies substrate phosphorylation activity catalyzed by a PK polypeptide under phosphorylation conditions in the presence or absence of a test compound that can bind to the PK and potentially inhibit the PK phosphorylation activity. A suitable substrate can be utilized in an assay, such as a polypeptide or peptide substrate, for example. A peptide substrate for assessing ABL1 inhibitor activity can contain the amino acid sequence EAIYAAPFAKKK (SEQ ID NO:7), for example. An assay for quantifying substrate phosphorylation activity inhibition sometimes outputs one or more of an IC50 value, Ki value, Kd value, Koff value and Kon value as a quantification of PK inhibition and/or binding. A non-limiting example of an assay for quantifying substrate phosphorylation activity inhibition analyzes a peptide substrate capable of being phosphorylated by a PK polypeptide, referred to herein as an "PK peptide substrate." A PK peptide substrate sometimes is labeled with one or more detectable labels (for example, a fluorescent agent). Fluorescence from a PK peptide substrate labeled with a fluorescent agent sometimes is assessed in an assay. In certain embodiments, a PK peptide substrate end-labelled with a distinct donor fluorophore on one end and a distinct acceptor fluorophore on the other end is utilized. In certain instances, the donor and the acceptor fluorophores are a Fluorescence Resonance Energy Transfer (FRET) pair. In certain embodiments, the donor fluorophore is coumarin and the acceptor fluorophore is fluorescein. In certain instances, a PK peptide substrate is cleaved in an assay after the peptide is exposed to phosphorylation conditions. An assay in which a PK peptide substrate is labeled with one or more detection agents and exposed to cleavage conditions is referred to as a "labeled peptide cleavage assay" and “peptide cleavage assay.” In certain embodiments, a labeled peptide cleavage assay includes: (1) contacting an unphosphorylated peptide, labeled at each end with a FRET pair fluorophore, with a test compound and a PK polypeptide having a PK phosphorylation activity, under phosphorylation conditions, thereby generating a phosphorylated peptide; (2) exposing the peptide, after (1), to phosphorylation state-dependent cleavage conditions, thereby generating cleaved peptide; and (3) measuring and
analyzing, after (2) a fluorescent emission signal from one or both fluorophores. A non-limiting example of a labeled peptide cleavage assay is described in Example 9 (Z’LYTE™ assay). Under phosphorylation conditions, a PK polypeptide typically is capable of transferring a phosphate from a provided cofactor (for example, adenosine triphosphate (ATP)) to the substrate (for example, peptide or protein substrate), where presence of a PK inhibitor compound reduces the amount of substrate phosphorylation compared to conditions in which the compound is not present. Under phosphorylation state-dependent cleavage conditions, (i) the phosphorylated substrate, but not the unphosphorylated substrate, is capable of being cleaved, or (ii) the phosphorylated substrate is preferentially cleaved relative to the unphosphorylated substrate, or (iii) the unphosphorylated substrate, but not the phosphorylated substrate, is capable of being cleaved, or (iv) the unphosphorylated substrate is preferentially cleaved relative to the phosphorylated substrate. The substrate typically is exposed to cleavage conditions after the substrate is contacted with a PK polypeptide under phosphorylation conditions. The substrate can be cleaved by a peptidase or protease enzyme under cleavage conditions. After the substrate is exposed to phosphorylation conditions and cleavage conditions, a fluorescent signal from cleaved substrate can be measured. In certain embodiments for a substrate containing a donor and acceptor FRET pair, a ratio of donor emission to acceptor emission (or a ratio of acceptor emission to donor emission) after excitation of the donor can be determined to assess the degree of peptide cleavage and thereby degree of peptide phosphorylation. An IC50 value can be determined from such a ratio as known in the art. Another type of assay involving FRET is a tracer displacement assay, a non-limiting example of which is described in Example 9 (LanthaScreen™ Eu Kinase Binding Assay). A tracer binding assay measures test compound binding to a PK. In a tracer displacement assay, a PK is contacted with (i) a tracer ligand, labeled with a FRET pair fluorophore, that binds to the PK under binding conditions; (ii) a test molecule that displaces the tracer ligand when the test molecule binds to the PK under the binding conditions; and (iii) an antibody, conjugated to another FRET pair fluorophore, that binds to the PK. Binding of the antibody and tracer ligand to the PK results in a FRET signal, and displacement of tracer ligand from the PK by a test molecule that competes with the tracer ligand for binding to the PK results in a reduction of the FRET signal. Another type of assay that can be utilized to quantify phosphorylation activity inhibition is an adenosine diphosphate (ADP) formation assay. The assay can be used to quantify ATP hydrolysis, including the intrinsic ATPase activity of a PK that transfers a terminal phosphate from ATP to water (and not a peptide substrate), thereby generating ADP from ATP. A non-limiting example of
an ADP formation assay is described in Kashem et al., J. Biomol. Screen.12:70-83 (2007) and is described in Example 9 (Adapta™ Assay). Another type of assay that can be utilized to quantify binding of a test compound to a PK is a solid phase inhibitor competition assay. The assay can be used to quantify binding of a test compound to a PK tagged with a nucleic acid detection tag in competition with a solid phase-associated PK inhibitor. The amount of the PK associated with the solid phase, assessed by PCR quantification of the detection tag, determines the level of PK binding to the test compound. A non-limiting example of a solid phase inhibitor competition assay is a KINOMEscan™ assay (EuroFins Discovery, described in Fabian et al., Nat. Biotechnol.23: 329-336 (2005) for example). Uses of compounds A compound can be used in a variety of applications. A compound can be used to (i) inhibit one or more PKs in vitro, ex vivo, or in vivo, (ii) inhibit one or more PKs in cells, organs and/or tissues administered a composition containing a compound; and/or (iii) inhibit one or more PKs in a subject administered a composition containing the compound. A compound can be utilized in studies, including, for example: (i) studies of PK inhibitors (for example, in vitro assay studies); (ii) pre- clinical in vivo animal studies, including xenograft studies in mice and pharmacokinetic studies in higher animals (for example, rats, dogs and/or monkeys); and (iii) human clinical studies. A compound herein can be utilized as a reference compound in a study of other compounds (for example, negative control or positive control), such as in an in vitro assay study, pre-clinical study and/or clinical study, for example. A compound herein can be (i) for treatment of a medical condition; (ii) prepared as a composition (for example, pharmaceutical composition) or medicament for treatment of a medical condition; and/or (iii) utilized in a method for treating a medical condition in which a compound is administered to a subject in need thereof in an amount sufficient to treat the medical condition (an effective amount). For embodiments in which a subject is treated, the subject can be human (homo sapiens) and can be an adult or pediatric patient. A medical condition sometimes is a PK-associated condition, such as a medical condition associated with a PK aberration and/or dysregulation of a PK (for example, dysregulation of a PK gene). A PK aberration can be a PK modification, which, for example, can be a nucleic acid translocation or other modification associated with a PK gene A PK modification can be outside of a PK gene coding region and result in dysregulation of the PK gene. A PK modification can be an addition, deletion or substitution of one or more amino acids in the PK encoded by a PK gene. A PK translocation can be within a PK gene coding region and result in a PK gene truncation and/or translocation of a PK gene or portion thereof to a different chromosome or different location of the same chromosome. A PK translocation can result in a fusion of a PK
gene or portion thereof with another nucleic acid portion from a different chromosome or different location of the same chromosome. A PK aberration can result in an altered PK activity relative to the PK activity when the aberration is not present. An altered activity can be (i) altered binding affinity to an inhibitor, (ii) altered binding activity to a native binding partner, and/or (iii) increased phosphorylation activity due to PK overexpression or increased intrinsic activity, for example. A PK- associated medical condition can be caused by an aberration of (for example, dysregulation and/or modification of) one or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. A medical condition sometimes is a cell proliferative condition such as a cancer for example, and a compound can be used to treat a cancer condition. A compound can be used to treat a cancer condition associated with one or more PK modifications, including modification of one or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. Non-limiting examples of cancers include lymphomas, thymomas, leukemias, carcinomas, gliomas, sarcomas (including liposarcoma), adenocarcinomas, adenosarcomas, and adenomas. Non-limiting examples of cancers are cancers occurring in lymph nodes, blood, thymus, breast, heart, lung, small intestine, colon, rectum, spleen, kidney, bladder, head, neck, esophagus, ovary, prostate, brain, pancreas, skin, bone, bone marrow, uterus, testicles, cervix and liver. Cancers include leukemia or lymphoid malignancies, hematologic malignancies, such as Hodgkin's lymphoma; non-Hodgkin's lymphomas, including Burkitt's lymphoma, small lymphocytic lymphoma/chronic lymphocytic leukemia, mycosis fungoides, mantle cell lymphoma, follicular lymphoma, diffuse large B-cell lymphoma, marginal zone lymphoma, hairy cell leukemia and lymphoplasmacytic leukemia; tumors of lymphocyte precursor cells, including B-cell acute lymphoblastic leukemia/lymphoma and T-cell acute lymphoblastic leukemia/lymphoma; thymoma; tumors of the mature T and NK cells, including peripheral T-cell leukemias, adult T-cell leukemia/T- cell lymphomas and large granular lymphocytic leukemia; Langerhans cell histocytosis; a myeloid neoplasia including acute myelogenous leukemia (AML), AML with maturation, AML without differentiation, acute promyelocytic leukemia, acute myelomonocytic leukemia, and acute monocytic leukemias; myelodysplastic syndromes; and chronic myeloproliferative disorders, including chronic myelogenous leukemia. Cancers include colorectal and head and neck tumors; squamous cell carcinoma of the head and neck; brain tumors such as glioblastomas; tumors of the lung, breast, pancreas, esophagus, bladder, kidney, ovary, cervix, and prostate; central nervous system neoplasms; neuroblastomas;
capillary hemangioblastomas; meningiomas and cerebral metastases; melanoma; gastrointestinal and renal carcinomas and sarcomas; rhabdomyosarcoma; glioblastoma, including glioblastoma multiforme; leiomyosarcoma; lymphoma; blastoma; neuroendocrine tumors; mesothelioma; schwannoma; meningioma; tumors of the central nervous system, including glioma, glioblastoma, neuroblastoma, astrocytoma, medulloblastoma, ependymoma, and retinoblastoma; solid tumors of the head and neck, including nasopharyngeal cancer, salivary gland carcinoma, and esophageal cancer; a lung cancer including small-cell lung cancer, non-small cell lung cancer (NSCLC), adenocarcinoma of the lung and squamous carcinoma of the lung; a digestive system cancer, gastric cancer or stomach cancer, including gastrointestinal cancer, cancer of the bile duct or biliary tract, colon cancer, colon adenocarcinoma, rectal cancer, colorectal cancer, and anal carcinoma; a reproductive system cancer including testicular, penile, or prostate cancer, uterine, vaginal, vulval, cervical, ovarian, and endometrial cancer; thyroid cancer, including medullary thyroid cancer (MTC), thyroid gland medullary carcinoma, papillary thyroid cancer (PTC); skin cancer, including melanoma, cutaneous carcinoma, basal cell carcinoma, squamous cell cancer, actinic keratosis; liver cancer, including hepatic carcinoma, hepatocellular cancer, and hepatoma; bone cancer, including osteoclastoma, and osteolytic bone cancers; cancer of additional tissues and organs, including pancreatic cancer, bladder cancer, kidney or renal cancer, breast cancer, cancer of the peritoneum, and Kaposi's sarcoma; tumors of the vascular system, including angiosarcoma and hemangiopericytoma; and blood cancers including leukemia, myelodysplastic syndrome (MDS), myelofibrosis, polycythemia vera and essential thrombocythemia. A cancer can be treated with a composition containing a compound herein as an active ingredient, and in certain embodiments a composition used to treat a cancer contains a compound of Subgroup 1 or Subgroup 5. Particular blood cancers include leukemias, and leukemias include chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL). A CML that can be treated includes chronic phase CML (CML-CP), acute phase CML (CML-AP) and blast phase CML (CML-BP). An ALL that can be treated includes a relapsed and/or refractory ALL (R/R ALL), Philadelphia chromosome-positive ALL, and other forms of ALL described herein (for example, Philadelphia chromosome-positive-like- ALL, B-ALL, T-ALL). A leukemia sometimes is associated with an ABL family PK aberration, and sometimes an ABL1 PK aberration. A compound that inhibits an ABL family PK (for example, an ABL1 PK) can be used to treat a leukemia (for example, CML and/or an ALL such as Philadelphia chromosome-positive ALL). A compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally JAK1, can be used to treat a leukemia (for example, a CML and/or an ALL such as Philadelphia chromosome-positive ALL). A compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, AURKA, JAK2 and JAK3, and optionally mildly inhibits or
ineffectively inhibits JAK1, can be used to treat a leukemia (for example, a CML and/or an ALL). A compound that effectively inhibits or moderately inhibits one or more of all of TYK2, a TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F can be used to treat a leukemia (for example, a CML and/or an ALL such as Philadelphia chromosome-positive ALL). A leukemia, such as CML and/or an ALL for example, can be treated with a compound of Subgroup 1. For example, a Philadelphia chromosome-positive ALL and/or R/R Philadelphia chromosome-positive ALL, can be treated with a compound of Subgroup 1. A leukemia can be a Philadelphia chromosome-positive-like ALL, which has been associated with a rearrangement involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, NTRK3, PDGFRB, PTK2B, TSLP and/or TYK2 and/or a sequence mutations involving FLT3, IL7R and/or SH2B3 (see, for example, Roberts et al., N Engl J Med 371(11): 1005-1015 (2014)). A compound that effectively inhibits or moderately inhibits ABL2, TYK2, TRKC and PTK2B, can be used to treat a Philadelphia chromosome-positive-like ALL. A compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally JAK1, can be used to treat a Philadelphia chromosome-positive-like ALL. A compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally mildly inhibits or ineffectively inhibits JAK1, can be used to treat a Philadelphia chromosome-positive-like ALL. A compound that effectively inhibits or moderately inhibits one or more of all of TYK2, a TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F can be used to treat a Philadelphia chromosome-positive-like ALL. A Philadelphia chromosome-positive-like ALL can be treated with a compound of Subgroup 1. A leukemia can be a B-cell acute lymphoblastic leukemia (B-ALL). A B-ALL can be a TCF3-HLF- positive B-ALL, which can be a TCF3-HLF-positive acute B-ALL. A TCF3-HLF-positive B-ALL typically is a B-ALL harboring a t(17;19)(q22;p13) translocation, producing an aberrant TCF3-HLF fusion (see, for example, Leonard et al., Haematologica 106(11): 2990-2994 (2021)). A TCF3-HLF- positive B-ALL can be associated with an AURKA aberration, and a compound that effectively inhibits or moderately inhibits an AURKA PK can be used to treat a B-ALL, such as a TCF3-HLF- positive B-ALL for example. A compound that effectively inhibits or moderately inhibits ABL1, ABL1- T315I, BTK, AURKA, JAK2 and JAK3, and optionally JAK1, can be used to treat a B-ALL, such as a TCF3-HLF-positive B-ALL for example. A compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2 and JAK3, and optionally mildly inhibits or ineffectively inhibits JAK1, can be used to treat a B-ALL, such as a TCF3-HLF-positive B-ALL for example. A compound that effectively inhibits or moderately inhibits ABL1, ABL1-T315I, BTK, AURKA, JAK2, NTRK3 (for example, a ETV6–NTRK3 fusion), PTK2B, TYK2 and ABL2 can be used to treat a B- ALL, such as a TCF3-HLF-positive B-ALL for example, where the compound optionally can
effectively inhibit or moderately inhibit JAK1 or the compound optionally can mildly inhibit or ineffectively inhibit JAK1. A compound that effectively inhibits or moderately inhibits one or more of all of TYK2, a TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F can be used to treat a B-ALL, such as a TCF3-HLF-positive B-ALL for example. A B- ALL, including a TCF3-HLF-positive B-ALL for example, can be treated with a compound of Subgroup 1. A subject identified as having an ABL1-T315I variant can be treated with a compound herein (for example, for treatment of a leukemia such as a CML and/or an ALL such as Philadelphia chromosome-positive ALL). A subject not identified as having an ABL1-T315I variant or identified as not having an ABL1-T315I variant, and is resistant and/or intolerant to at least two PK inhibitors, can treated with a compound herein (for example, for treatment of a leukemia such as a CML and/or ALL such as Philadelphia chromosome-positive ALL). A subject having no available protein kinase inhibitor options can be administered a compound herein to treat CML. A compound that inhibits a TRK family PK can be utilized to treat a cancer associated with a TRK family PK aberration. A cancer sometime is a cancer positive for a TRK family PK fusion. In certain instances, the cancer is a solid tumor positive for a TRK family PK fusion, and optionally where the TRK portion of the fusion does not contain a known acquired resistance amino acid substitution. A compound that inhibits a ROS family PK can be utilized to treat a cancer associated with a ROS family PK aberration. In certain instances, the cancer is a ROS1 positive lung cancer, including without limitation a solid tumor and/or a lung cancer. A ROS1 positive lung cancer can be a lung nodule cancer, non-small cell lung cancer, small cell lung cancer or mesothelioma. A compound that inhibits an EPH family PK can be utilized to treat a cancer associated with an EPH family PK aberration. In certain instances, the cancer is associated with an EPHA1 aberration, EPHA2 aberration and/or an EPHB1 aberration, non-limiting examples of which include a breast cancer, lung cancer, brain cancer, spinal cancer, gastric cancer, or skin cancer, and optionally a solid tumor cancer. In certain instances, the lung cancer is non-small cell lung cancer (NSCLC); the skin cancer is myeloma; and the brain cancer or spinal cancer is a glioblastoma. A compound that inhibits a TNK family PK can be utilized to treat a cancer associated with a TNK family PK aberration. In certain instances, a cancer is associated with a TNK1 PK aberration, such as a cancer deficient in LKB1, for example. In certain instances, a cancer associated with a TNK1 aberration is a cancer associated with a TNK1 variant to which binding of a 14-3-3 protein is weaker than to TNK1(wt), a non-limiting example of which is Hodgkin lymphoma, for which the Hodgkin lymphoma cell line L540 can be representative.
A compound that inhibits a JAK family PK can be utilized to treat a medical condition associated with a JAK family PK aberration (a JAK-associated medical condition). A JAK-associated medical condition sometimes is a JAK2-associated medical condition, and compound that selectively inhibits a JAK2 PK is used to treat the medical condition. In certain embodiments, a JAK2- associated medical condition is a cancer, including without limitation, a lung cancer, breast cancer, head cancer or neck cancer. In certain embodiments, a JAK2-associated medical condition is a blood cancer, including without limitation, myelodysplastic syndrome (MDS), myelofibrosis, polycythemia vera or essential thrombocythemia. In certain instances, a JAK2-associated cancer is positive for a JAK2 variant containing a V617F substitution. A compound that inhibits a RET family PK can be utilized to treat a cancer associated with a RET family PK aberration (for example, a cancer associated with a RET family PK fusion). In certain instances, a cancer associated with a RET family PK is lung cancer, including non-small cell lung cancer (NSCLC) and/or lung adenocarcinoma; a thyroid cancer, including medullary thyroid cancer (MTC), thyroid gland medullary carcinoma and/or papillary thyroid cancer (PTC); a colon cancer, including colon adenocarcinoma; and/or a skin cancer including melanoma and/or cutaneous melanoma. A compound utilized to treat a cancer associated with a RET family PK sometimes is a Subgroup 2 compound. A compound that inhibits a PLK4 family PK can be utilized to treat a cancer associated with a PLK family PK aberration. In certain instances, a cancer is associated with a PLK4 aberration, non- limiting examples of which include liver cancer, breast cancer and AML. A compound utilized to treat a cancer associated with a PLK4 family PK sometimes is a Subgroup 2 compound. A compound that inhibits an IRAK family PK can be utilized to treat a cancer associated with an IRAK family PK aberration. In certain instances a cancer is associated with an IRAK3 aberration. A compound can be used to treat minimum residual disease (MRD) associated with a cancer condition, and can be a compound that inhibits a JAK family PK. A compound that is an effective inhibitor, or optionally a moderate inhibitor, of a JAK PK can be used to treat a cancer condition with potentially higher efficacy, as compared to treatment of the condition with a compound that is not an effective inhibitor or not a moderate inhibitor of a JAK PK. A compound that is an effective inhibitor of, or moderate inhibitor of, a JAK family PK, and an effective inhibitor of or moderate inhibitor of one or more other family PKs, can be used to treat, with potentially high efficacy, a cancer associated with the one or more other family PKs. For example, a compound that is an effective inhibitor of a JAK family PK and of an ABL family PK can be used to treat an ABL1- associated blood cancer, including CML and Philadelphia chromosome-positive ALL, for example,
with potentially higher efficacy than a compound that effectively inhibits the ABL family PK but not the JAK family PK. In certain embodiments, a compound is used to treat an inflammation condition, autoimmune condition and/or skin condition. In certain instances, the inflammation condition is a chronic inflammation condition and/or senescent cell chronic inflammation condition such as a senescence- associated secretory phenotype (SASP) condition, for example. In certain instances, the autoimmune condition is atopic dermatitis, non-segmental vitiligo or rheumatoid arthritis. In certain instances, the rheumatoid arthritis is intolerant to one or more tumor necrosis factor (TNF) blockers. In certain instances, the skin condition is atopic dermatitis, non-segmental vitiligo, psoriasis (for example, plaque psoriasis), ultraviolet (UV) damaged skin, severely UV damaged skin or aged skin. A topical cream containing a compound can be used to treat a inflammation condition, autoimmune condition or skin condition. In certain embodiments, a compound is used to treat a medical condition associated with a TYK family PK aberration, such as a medical condition associated with a TYK2 PK aberration. In certain embodiments, a compound is used to treat psoriasis, which can be moderate to severe psoriasis. In certain embodiments, a compound is used to treat plaque psoriasis, which can be moderate to severe plaque psoriasis. In certain instances, a compound is used to treat a subject who is a candidate for systemic therapy or phototherapy. In certain embodiments, the compound inhibits a TYK family PK, and in certain instances, the compound inhibits TYK2(wt). In certain embodiments, the compound is a Subgroup 3 compound. A compound that is an effective inhibitor and selective inhibitor of a JAK2 PK can be used to treat a condition with a potentially lower incidence of a serious adverse event, as compared to treatment of the condition with a compound that is not a selective inhibitor of a JAK2 PK. Non-limiting examples of compounds that are not selective inhibitors of JAK2 PK are tofacitinib or ruxolitinib. A serious adverse event can be a malignancy, serious adverse cardiovascular event and/or blood clot, mortality or infection. In certain embodiments, a compound that is an effective inhibitor and selective inhibitor of a JAK2 PK can be utilized to treat a condition in a subject having a prior history of heart disease, and to whom a compound that is not a selective inhibitor of JAK2 would not be administered. A moderate to severe form of a medical condition can be treated. For example, moderate to severe rheumatoid arthritis or moderate to severe plaque psoriasis can be treated. A stage III or stage IV cancer condition can be treated (for example, a stage IV ROS1 positive lung cancer), for example. A medical condition associated with a particular variant PK can be treated. In certain instances, a blood cancer, such as myelofibrosis, MDS, polycythemia vera or essential thrombocytopenia, for
example, can be treated in subjects from which a sample was assessed as having a JAK2 containing a V617F variation. Such subjects can be treated with a compound that effectively inhibits a JAK2 variant containing the V617F. In certain instances, a leukemia, such as CML or Philadelphia chromosome-positive ALL, for example, can be treated in subjects from which a sample was assessed as having an ABL1 variant containing a T315I substitution. Such subjects can be treated with a compound that effectively inhibits an ABL1 variant containing a T315I substitution, such as a compound of Subgroup 1, for example. In certain embodiments, it is determined whether a PK having a particular variation (a PK variant) is present or absent in a sample from a subject, and if the PK variant is identified as being present in the sample, then a particular medical condition associated with the PK variant is treated. In certain instances, presence or absence of a JAK2 variant containing a V617F substitution is screened in a sample from a subject, and if the variant is present in the sample, the subject may be treated for a particular medical condition associated with the variant (for example, a blood cancer such as myelofibrosis, MDS, polycythemia vera or essential thrombocytopenia, for example). In certain instances, presence or absence of an ABL1 variant containing a T315I substitution is screened in a sample from a subject, and if the variant is present in the sample, the subject may be treated for a particular medical condition associated with the variant (for example, a leukemia such as CML or Philadelphia chromosome-positive ALL, for example). In certain instances, presence or absence of a DDR2 variant containing N456S and/or T654M substitution is screened in a sample from a subject, and if the variant is present in the sample, the subject may be treated for a particular medical condition associated with the variant (for example, a lung cancer such as non-small cell lung cancer (NSCLC)). In certain instances, presence or absence of a RET variant containing one or more of A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F is screened in a sample from a subject, and if the variant is present in the sample, the subject may be treated for a particular medical condition associated with the variant (for example, a lung cancer (NSCLC) or thyroid cancer (medullary thyroid cancer (MTC), papillary thyroid cancer (PTC) or thyroid gland medullary carcinoma, for example)). A compound typically is utilized in an amount sufficient to inhibit a PK activity (an effective amount). An “effective amount” often is a dosage sufficient to affect a beneficial or desired result. Non- limiting examples of desired results include reducing a PK activity (e.g., test compound binding activity; substrate phosphorylation activity); decreasing, attenuating and/or stabilizing one or more symptoms associated with a condition; increasing quality of life of a subject suffering from a condition; decreasing the dose of other medications required to treat the condition; enhancing the effect of another medication; delaying the progression of the condition; and/or prolonging survival of a subject. Non-limiting examples of symptoms associated with cancer include presence and/or
proliferation of cancer cells; presence and/or growth of one or more tumors; cancer metastases and the like. An effective amount can be an amount sufficient to: kill cancer cells; reduce the rate of cancer cell proliferation; and/or eliminate, reduce and/or delay metastasis from a primary site of cancer. An effective amount may be in conjunction with another therapeutic agent. An effective amount may be considered in the context of administering a compound described herein without another therapeutic agent or with another therapeutic agent. An optimal range of an effective amount of each component can be determined. An effective amount can be determined by standard clinical techniques and can be a technique for determining dosage. An effective amount often depends on the route of administration and the seriousness of the condition, and often is decided according to the judgment of the practitioner and circumstances of each subject. An effective amount can be administered in one or more administrations. Non-limiting types of administration include parenteral administration (e.g., intradermal, intramuscular, intraperitoneal, intravenous and subcutaneous), epidural, and mucosal (e.g., intranasal and oral routes). Administration may be by any suitable route, for example, by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, and the like), and may be by pulmonary administration (e.g., use of an inhaler or nebulizer, and formulation with an aerosolizing agent). An effective amount may be delivered by liposomes, microparticles and/or microcapsules in certain implementations. An effective dosage of an active ingredient can be determined by assessing its in vitro activity in a cell or tissue system and/or in vivo activity in an animal system. For example, methods for extrapolating an effective dosage in mice and other animals to humans are known (see, for example, U.S. Pat. No.4,938,949). Such systems can be used for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population) of an active ingredient. The dose ratio between a toxic and therapeutic effect is the therapeutic index and it can be expressed as the ratio ED50/LD50. A dosage of an active ingredient often lies within a range of circulating concentrations for which the ED50 is associated with low toxicity or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. A therapeutically effective dose of an active ingredient can be estimated initially from cell culture assays. A dose sometimes is formulated to achieve a circulating plasma concentration range covering the IC50 (for example, the concentration of an active ingredient that achieves a half-maximal inhibition of a symptom) as determined in in vitro assays, as such information often is used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid
chromatography and/or a spectrometric process (for example, liquid chromatography and mass spectrometry (for example, LCMS)). Another example of determining an effective dose for a subject is to directly assay levels of "free" and "bound" levels of an active ingredient in the serum of the test subject. Such assays may utilize antibody mimics and/or "biosensors" generated by molecular imprinting techniques. The active ingredient is used as a template, or "imprinting molecule", to spatially organize polymerizable monomers prior to their polymerization with catalytic reagents. Subsequent removal of the imprinted molecule leaves a polymer matrix that contains a repeated "negative image" of the active ingredient and is able to selectively rebind the molecule under biological assay conditions (see, for example, Ansell, et al., Current Opinion in Biotechnology (1996) 7:89-94 and in Shea, Trends in Polymer Science (1994) 2:166-173). Such "imprinted" affinity matrixes are amenable to ligand-binding assays, whereby the immobilized monoclonal antibody component is replaced by an appropriately imprinted matrix (see, for example, Vlatakis, et al., Nature (1993) 361:645-647). Through the use of isotope-labeling, "free" concentration of an active ingredient can be readily monitored and used in calculations of IC50. Such "imprinted" affinity matrixes can also be designed to include fluorescent groups having photon-emitting properties that measurably change upon local and selective binding of an active ingredient. These changes can be readily assayed in real time using appropriate fiberoptic devices, in turn allowing the dose in a test subject to be quickly optimized based on its individual IC50. An example of such a "biosensor" is addressed in Kriz, et al, Analytical Chemistry (1995) 67:2142- 2144. Non-limiting examples of doses include milligram or microgram amounts of an active ingredient per kilogram of subject or sample weight, for example, about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about 1 microgram per kilogram to about 50 micrograms per kilogram. It is understood that appropriate doses of a small molecule depend upon the potency of the small molecule with respect to the expression or activity to be modulated. When one or more of these small molecules is to be administered to an animal (for example, a human) in order to modulate expression or activity of a polypeptide or nucleic acid described herein, a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained. In addition, it is understood that the specific dose level for any particular animal subject will depend upon a variety of factors including the activity of the specific active ingredient employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.
Certain Implementations Following are non-limiting examples of certain implementations of the technology. A1. A composition comprising a compound of Formula A: R2 R1 R3 Formula A
wherein: R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R4, R5 and R6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo. A2. The composition of embodiment A1, wherein R1, R2 and R3 each independently is hydrogen, methyl or methoxy. A3. The composition of embodiment A1 or A2, wherein R4, R5 and R6 each independently is hydrogen, F, isopropyl, or isopropyloxy. A4. The composition of any one of embodiments A1-A3, wherein one of R1, R2 and R3 is methyl or methoxy and the other two of R1, R2 and R3 are hydrogen. A5. The composition of any one of embodiments A1-A4, wherein R1, R2 and R3 each is hydrogen. A6. The composition of any one of embodiments A1-A5, wherein R5 is hydrogen. A7. The composition of any one of embodiments A1-A6, wherein R4, R5 and R6 each is hydrogen. A8. The composition of any one of embodiments A1-A7, wherein R1 is methyl or methoxy and R2 and R3 each is hydrogen. A9. The composition of any one of embodiments A1-A8, wherein R1 is methyl and R2 and R3 each is hydrogen. A10. The composition of any one of embodiments A1-A7, wherein R3 is methyl or methoxy and R1 and R2 each is hydrogen.
A11. The composition of any one of embodiments A1-A7 and A10, wherein R3 is methyl and R1 and R2 each is hydrogen. A12. The composition of embodiment A1, where R1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R2, R3 and R5 each is hydrogen; and R4 and R6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo, with the proviso that R4 or R6 , or R4 and R6, is not hydrogen. A13. The composition of embodiment A12, where R1 is an unsubstituted C1-C4 alkyl, ethyl or methyl. A14. The composition of embodiment A12 of A13, where (i) R4 is unsubstituted C1-C4 alkoxy or isopropyloxy; (ii) R6 is fluoro or chloro; or a combination of (i) and (ii). A15. The composition of any one of embodiments A12-A14, where the compound is 4-((5-((8-(4- fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C1); 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid (compound C3); 4-((5-((8-(2-isopropylphenyl)quinazolin-2- yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C4); or a pharmaceutically acceptable salt thereof. A16. The composition of embodiment A1, where R1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R2, R3, R4, R5 and R6 each is hydrogen. A17. The composition of embodiment A16, where R1 is an unsubstituted C1-C4 alkyl, ethyl or methyl. A18. The composition of embodiment A16 or A17, where the compound is 4-((2-methyl-5-((8- phenylquinazolin-2-yl)amino)phenyl)carbamoyl)benzoic acid or a pharmaceutically acceptable salt thereof. A19. The composition of embodiment A1, where R3 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R1, R2, R4, R5 and R6 each is hydrogen. A20. The composition of embodiment A19, where R3 is an unsubstituted C1-C4 alkyl, ethyl or methyl. A21. The composition of embodiment A19 or A20, where the compound is 4-((4-methyl-3-((8- phenylquinazolin-2-yl)amino)phenyl)carbamoyl)benzoic acid (compound C13) or a pharmaceutically acceptable salt thereof. B1. A composition comprising a compound of Formula B:
R2 O R1 R3 N B
R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R7, R8 and R9 each independently is hydrogen or optionally substituted C1-C6 alkyl. B2. The composition of embodiment B1, wherein R1, R2 and R3 each independently is hydrogen, methyl or methoxy. B3. The composition of embodiment B1 or B2, wherein R7, R8 and R9 each independently is hydrogen or isobutyl. B4. The composition of any one of embodiments B1-B3, wherein one of R1, R2 and R3 is methyl or methoxy and the other two of R1, R2 and R3 are hydrogen. B5. The composition of any one of embodiments B1-B4, wherein R1, R2 and R3 each is hydrogen. B6. The composition of any one of embodiments B1-B4, wherein R8 and R9 each is hydrogen. C1. The composition of any one of embodiments A1-A21 or B1-B6, with the proviso that R1 and R2, or optionally R2 and R3, do not join to form an imidazolyl group. C1.1. The composition of any one of embodiments A1-A21, B1-B6 and C1, with the proviso that R1 is not heterocycloalkyl or substituted heterocycloalkyl. C1.2. The composition of any one of embodiments A1-A21, B1-B6 and C1, with the proviso that R1 does not contain a heterocycloalkyl or substituted heterocycloalkyl. C1.3. The composition of any one of embodiments A1-A21, B1-B6 and C1, wherein R1 is hydrogen. C1.4. The composition of any one of embodiments A1-A21, B1-B6 and C1, with the proviso that R6 is not methoxy. C1.5. The composition of any one of embodiments A1-A21, B1-B6 and C1,with the proviso that R5 and/or R6 is not:
O N O H N O H H H3C H 3C N O H3C N O N N N H 3 C S S S R4,
R4, R5, R6, R7 , R8 or R9 is not (i) one of the following designated Group A electrophilic groups: ;
or (ii) one of the following designated Group B electrophilic groups:
or (iii) an electrophilic group capable of forming a covalent bond with a cysteine of a protein. C1.8. The composition of any one of embodiments A1-A21, B1-B6 and C1, with the proviso that R2 and R3, or optionally R3 and R4, do not join to form an imidazolyl or substituted imidazolyl. C1.9. The composition of any one of embodiments A1-A21, B1-B6 and C1, with the proviso that R1 and R2, or optionally R2 and R3, do not join to form a heteroaryl containing 5 ring atoms or a substituted heteroaryl containing 5 ring atoms. C2. A composition comprising 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C3. A composition comprising 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-5- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C4. A composition comprising 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C5. A composition comprising 4-((5-((8-(2-isopropylphenyl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C6. A composition comprising 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof.
C7. A composition comprising 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C8. A composition comprising 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C9. A composition comprising 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C10. A composition comprising 4-((4-methyl-3-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C11. A composition comprising 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-4- methylphenyl)carbamoyl)benzoic acid, or a pharmaceutically acceptable salt thereof. C12. The composition of any one of embodiments A1-A21, B1-B6 and C1-C12, where the composition comprises a pharmaceutically acceptable salt of the compound, and the salt is a hydrochloride salt. D1. A composition comprising a compound of Formula D: R2 R1 R3 Formula D
R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R10, R11, R12 and R13 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy; m is an integer of 1 or 2; R14 is methyl or ;
n an 1 to 10; and
R15 is hydrogen, optionally substituted alkyl or optionally substituted alkylamido. D2. The composition of embodiment D1 or D2, wherein R1, R2 and R3 each independently is hydrogen, methyl or methoxy. D4. The composition of any one of embodiments D1-D3, wherein one of R1, R2 and R3 is methyl or methoxy and the other two of R1, R2 and R3 are hydrogen. D5. The composition of any one of embodiments D1-D4, wherein R1, R2 and R3 each is hydrogen. D6. The composition of any one of embodiments D1-D5, wherein R10, R11, R12 and R13 each independently is hydrogen or methoxy. D7. The composition of any one of embodiments D1-D6, wherein R10 and R12 each is hydrogen. D8. The composition of any one of embodiments D1-D7, wherein R11 and R13 each is methoxy. D9. The composition of any one of embodiments D1-D8, wherein m is the integer 2. D10. The composition of any one of embodiments D1-D9, wherein R14 is O .
of any one of embodiments D1-D10, wherein n is an integer of 3 to 7. D12. The composition of any one of embodiments D1-D11, with the proviso that R12 is not methoxy. D13. A composition comprising a compound of the following formula: .
a compound of the following formula:
. nd of the following formula: .
formula: .
any one the proviso that R1 is not heterocycloalkyl or substituted heterocycloalkyl. D18. The composition of any one of embodiments D1-D16, with the proviso that R1 does not contain a heterocycloalkyl or substituted heterocycloalkyl. D19. The composition of any one of embodiments D1-D16, wherein R1 is hydrogen. D20. The composition of any one of embodiments D1-D16, with the proviso that R11 and/or R12 is not
O H N O H H 3C H N O H3C N O O H C N N N N H 3 C S S 3 S or
- CH2C(OH)(CH3)CH3, or -CH2CH2F. D21. The composition of any one of embodiments D1-D16, with the proviso that R10, R11, R12 or R13 is not .
of any one of embodiments D1-D16, with the proviso that R10, R11, R12 or R13 is not (i) one of the following designated Group A electrophilic groups: ;
or (ii) one of the following designated Group B electrophilic groups:
or (iii) an electrophilic group capable of forming a covalent bond with a cysteine of a protein. D23. The composition of any one of embodiments D1-D16, with the proviso that R10, R11, R12 or R13 is not an electrophilic group capable of forming a covalent bond with an electrophile. D24. The composition of any one of embodiments D1-D16, with the proviso that R2 and R3, or optionally R3 and R4, do not join to form an imidazolyl or substituted imidazolyl. D25. The composition of any one of embodiments D1-D16, with the proviso that R1 and R2, or optionally R2 and R3, do not join to form a heteroaryl containing 5 ring atoms or a substituted heteroaryl containing 5 ring atoms. D26. The composition of any one of embodiments D1-D16, with the proviso that R14 is not a phenyl or substituted phenyl. D27. The composition of any one of embodiments D1-D16, with the proviso that R14 and the N to which it is covalently attached do not together form unsubstituted morpholino or R49
where R49 is methyl, ethyl, methoxy, -C(O)CH3, -CH2CH2OH, -CH2CH2OCH3, -CH2CH(OH)CH3, - CH2C(OH)(CH3)CH3, or -CH2CH2F. D28. The composition of any one of embodiments D1-D16, with the proviso that R14 and the N to which it is covalently attached do not together form a heterocycloalkyl containing an N ring atom, or an O ring atom, or N and O ring atoms, or a substituted heterocycloalkyl containing an N ring atom, or an O ring atom, or N and O ring atoms. D29. The composition of any one of embodiments D1-D16, with the proviso that R14 and the N to which it is covalently attached do not together form a heterocycloalkyl or substituted heterocycloalkyl. D30. The composition of any one of embodiments D1-D16, with the proviso that R14 and the N to which it is covalently attached do not together contain a heterocycloalkyl or substituted heterocycloalkyl. D31. The composition of any one of embodiments D1-D16, with the proviso that R14 is not a heterocycloalkyl or substituted heterocycloalkyl. D32. The composition of any one of embodiments D1-D16, with the proviso that R14 does not contain a heterocycloalkyl or substituted heterocycloalkyl. E1. The composition of any one of embodiments A1-A21, B1-B6, C1-C12 and D1-D32 which is a pharmaceutical composition. E2. The composition of embodiment E1, where the compound is capable of inhibiting an activity of a protein kinase (PK). E3. The composition of embodiment E2, where the PK activity is a PK binding activity and/or a PK catalytic activity. E4. The composition of embodiment E2 or E3, where the compound is capable of inhibiting an activity of two or more PKs. E5. The composition of any one of embodiments E2-E4 where the compound is capable of effectively inhibiting, moderately inhibiting and/or selectively inhibiting a PK activity. E6. The composition of any one of embodiments E1-E5, which is a pharmaceutical composition comprising one or more pharmaceutically acceptable excipients. E7. The composition of embodiment E6, for topical administration, oral administration or administration by injection or infusion. F1. Use of a compound or composition of any one of embodiments A1-A21, B1-B6, C1-C12, D1- D32 and E1-E7 for inhibiting a protein kinase (PK).
F2. The use of embodiment F1, for effectively inhibiting or moderately inhibiting a PK. F3. Use of a composition comprising a compound, the compound comprising a quinazolinyl group and an amine-linked phenyl group for inhibiting two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and a PTK family PK. F4. Use of a composition comprising a compound comprising a quinazolinyl group and an amine- linked phenyl group for selectively inhibiting a JAK2 PK. F5. The use of embodiment F4, for effectively inhibiting JAK2(wt) PK and not effectively inhibiting JAK1(wt) PK. F6. The use of embodiment F4 or F5, for inhibiting a JAK3(wt) PK, optionally for effectively inhibiting a JAK3(wt) PK, and optionally for moderately inhibiting a JAK3(wt) PK. F7. The use of any one of embodiments F4-F6, for effectively inhibiting and/or moderately inhibiting two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and a PTK family PK. F8. The use of any one of embodiments F3-F7, where the composition comprises a compound of, or is a composition of, any one of embodiments A1-A21, B1-B6, C1-C12, D1-D32 and E1-E7. F9. The use of any one of embodiments F1-F8, for effectively inhibiting two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. F10. The use of embodiment f9, for moderately inhibiting two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family
PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. F11. The use of embodiment F9 or F10, for not effectively inhibiting and/or for not moderately inhibiting one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, a SRC family PK, a LCK family PK, a DDR family PK, and/or a PTK family PK. F12. The use of any one of embodiments F1-F11, for inhibiting an ABL family PK, optionally inhibiting ABL1(wt), optionally inhibiting one or more ABL1 variants, optionally inhibiting ABL2(wt), and/or optionally inhibiting one or more ABL2 variants; where the one or more ABL1 variants optionally comprise one or more of the following amino acid substitutions relative to ABL1(wt): T315I, G250E, Q252H, Y253F, E255K, F317L, M351T and H396P. F13. The use of any one of embodiments F1-F12, for effectively inhibiting ABL1, ABL1-T315I, AURKA, and JAK2. F14. The use of embodiment F13, for effectively inhibiting or moderately inhibiting BTK. F15. The use of embodiment F13 or F14, for effectively inhibiting or moderately inhibiting JAK3. F16. The use of any one of embodiments F13-F15, for effectively inhibiting or moderately inhibiting JAK1. F17. The use of any one of embodiments F13-F16, for mildly inhibiting or ineffectively inhibiting JAK1. F18. The use of any one of embodiments F13-F17, for effectively inhibiting or moderately inhibiting one or more or all of TYK2, A TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F. F19. The use of any one of embodiments F13-F18, for effectively inhibiting or moderately inhibiting one or more or all of TRKA, TRKB, TRKC, ROS1, EPHA1 and EPHB1. F20. The use of any one of embodiments F13-F19, for effectively inhibiting or moderately inhibiting a SRC family PK and/or a DDR family PK. F21. The use of any one of embodiments F13-F20, for effectively inhibiting or moderately inhibiting ABL2.
F22. The use of any one of embodiments F13-F21, for effectively inhibiting or moderately inhibiting PTK2B. F23. The use of any one of embodiments F1-F22, where the composition comprises a compound of any one of embodiments A1-A21 and B1-B6. F24. The use of any one of embodiments F1-F22, where the composition comprises a compound of any one of embodiments A12-A15. F25. The use of any one of embodiments F1-F22, for inhibiting, optionally effectively inhibiting or optionally moderately inhibiting, a TYK family PK. F26. The use of embodiment F25, for inhibiting, optionally effectively inhibiting or optionally moderately inhibiting TYK2(wt). F27. The use of any one of embodiments F1-F22, F25 and F26, for inhibiting a RET family PK, and optionally: inhibiting RET(wt) and/or one or more RET variants, where the one or more RET variants optionally comprise one or more of the following amino acid substitutions relative to RET(wt): A883F, G691S, M918T, S891A, V804E, V804L, V804M and Y791F. F28. The use of any one of embodiments F25-F27, where the composition comprises a compound of any one of embodiments A16-A18. F29. The use of any one of embodiments F1-F22 and F25-F27, for inhibiting a PLK family PK, and optionally: inhibiting PLK4(wt) and/or one or more PLK4 variants. F30. The use of embodiment F29, where the composition comprises a compound of any one of embodiments A19-A21. F31. The use of any one of embodiments F1-F30, for inhibiting a PK activity, optionally for inhibiting a PK binding activity, and/or optionally for inhibiting a PK phosphorylation activity. F32. The use of any one of embodiments F1-F30, where the PK is a homo sapiens PK. F33. The use of any one of embodiments F1-F31, which is in vitro or ex vivo. F34. The use of any one of embodiments F1-F31, which is in vivo. F35. The use of embodiment F33 or F34, which is in cells, an organ and/or a tissue. F36. The use of embodiment F34 or F35, which is in a subject. G1. Use of a compound or composition of any one of embodiments A1-A21, B1-B6, C1-C12, D1- D32 and E1-E7, for treatment of a medical condition or for preparation of a medicament for treatment of a medical condition.
G2. The use of any one of embodiments F1-F36 for treatment of a medical condition or for preparation of a medicament for treatment of a medical condition. G3. The use of embodiment G1 or G2, where the medical condition is associated with a protein kinase (PK) aberration. G4. The use of embodiment G3, where the medical condition is associated with dysregulation of a PK and/or is associated with a PK modification. G5. The use of embodiment G3 or G4, where the PK is one or more of, or two or more of, or three or more of, or four or more of, or five or more of, or six or more of, or seven or more of, or eight or more of, or nine or more of, or ten or more of, or eleven or more of, or twelve or more of, or thirteen or more of, or each of: an ABL family PK, a BTK family PK, a AURK family PK, a JAK family PK, a TRK family PK, a RET PK, an EPH family PK, a TNK family PK, a PLK family PK, an IRAK family PK, SRC family PK, DDR family PK, and/or PTK family PK. G6. The use of any one of embodiments G1-G5, where the medical condition is a cancer. G7. The use of embodiment G6, where the cancer is a lymphoma, thymoma, leukemia, carcinoma, glioma, sarcoma, liposarcoma, adenocarcinoma, adenosarcoma or adenoma. G8. The use of embodiment G6, where the cancer is a cancer occurring in one or more of blood, lymph node, thymus, thyroid, breast, heart, lung, small intestine, colon, rectum, spleen, kidney, bladder, head, neck, esophagus, ovary, prostate, brain, pancreas, skin, bone, bone marrow, uterus, testicles, cervix and liver. G9. The use of embodiment G8, where the cancer is a blood cancer. G10. The use of embodiment G9, where the blood cancer is a leukemia, myelodysplastic syndrome (MDS), myelofibrosis, polycythemia vera or essential thrombocythemia. G11. The use of embodiment G10, where the leukemia is acute myeloid leukemia (AML), chronic myeloid leukemia (CML) or acute lymphoblastic leukemia (ALL). G12. The use of embodiment G11, where the CML is chronic phase CML (CML-CP), acute phase CML (CML-AP) and blast phase CML (CML-BP). G13. The use of embodiment G11, where the ALL is a relapsed and/or refractory ALL (R/R ALL). G14. The use of embodiment G11 or G13, where the ALL is Philadelphia chromosome-positive ALL, Philadelphia chromosome-positive-like-ALL, B-cell acute lymphoblastic leukemia (B-ALL) or T-cell acute lymphoblastic leukemia (T-ALL). G15. The use of any one of embodiments G11, where the cancer is ALL and optionally the ALL is Philadelphia chromosome-positive ALL.
G16. The use of embodiment G14, where the ALL is Philadelphia chromosome-positive-like ALL. G17. The use of any one of embodiments G15 or G16, where the cancer is associated with an ABL family PK aberration and optionally an ABL1 family PK aberration. G18. The use of embodiment G17, where the compound effectively inhibits or moderately inhibits ABL1 and optionally ABL1-T315I. G19. The use of embodiment 14, where the cancer is a B-ALL, optionally is a TCF3-HLF-positive B-ALL, or optionally is a TCF3-HLF-positive acute B-ALL. G20. The use of embodiment G19, where the cancer is associated with an AURK family PK aberration. G21. The use of embodiment G19 or G20, where the compound effectively inhibits or moderately inhibits an AURKA family PK; and/or (ii) effectively inhibits or moderately inhibits an ABL1 family PK, optionally ABL1, and optionally ABL1-T315I. G22. The use of any one of embodiments G1-G8, where the cancer is a lung cancer. G23. The use of embodiment G22, where the lung cancer is NSCLC. G24. The use of embodiment G22 or G23, where the lung cancer is associated with a DDR family PK aberration and/or a SRC family PK aberration. G25. The use of embodiment G24, where the DDR family PK is a DDR2(wt) PK or DDR2 variant PK, and optionally the DDR2 variant PK optionally contains a N456S and/or T654M amino acid substitution. G26. The use of any one of embodiments G22-G25, where the compound (i) effectively inhibits or moderately inhibits SRC(wt), SCR-N1(wt), DDR2(wt) and/or a DDR2 variant containing a T654M and/or N456S amino acid substitution. G27. The use of any one of embodiments G1-G26, where the medical condition is treated in a subject identified as having an ABL1-T315I variant. G28. The use of any one of embodiments G1-G27, where the medical condition is treated in a subject not identified as having an ABL1-T315I variant or identified as not having an ABL1-T315I variant, and is resistant and/or intolerant to at least two PK inhibitors. G29. The use of any one of embodiments G1-G28, where the compound effectively inhibits ABL1, ABL1-T315I, AURKA, and JAK2. G30. The use of any one of embodiments G1-G29, where the compound effectively inhibits or moderately inhibits BTK.
G31. The use of any one of embodiments G1-G30, where the compound effectively inhibits or moderately inhibits JAK3. G32. The use of any one of embodiments G1-G31, where the compound effectively inhibits or moderately inhibits JAK1. G33. The use of any one of embodiments G1-G31, where the compound mildly inhibits or ineffectively inhibits JAK1. G34. The use of any one of embodiments G1-G33, where the compound effectively inhibits or moderately inhibits one or more or all of TYK2, A TRK family PK, ROS1, TXK, an EPH family PK, IRAK3, PLK4, TNK1, RET and JAK2-V617F. G35. The use of any one of embodiments G1-G34, where the compound effectively inhibits or moderately inhibits one or more or all of TRKA, TRKB, TRKC, ROS1, EPHA1 and EPHB1. G36. The use of any one of embodiments G1-G35, where the compound effectively inhibits or moderately inhibits a SRC family PK and/or a DDR family PK. G37. The use of any one of embodiments G1-G36, where the compound effectively inhibits or moderately inhibits ABL2. G38. The use of any one of embodiments G1-G37, where the compound effectively inhibits or moderately inhibits PTK2B. G39. The use of any one of embodiments G1-G38, where the a compound of any one of embodiments A1-A21 or optionally A12-A15. G40. The use of any one of embodiments G1-G8, where the cancer is a lung cancer, a thyroid cancer, a colon cancer or a skin cancer. G41. The use of embodiment G40, where: the lung cancer is a lung nodule cancer, non-small cell lung cancer (NSCLC), small cell lung cancer, lung adenocarcinoma or mesothelioma; the thyroid cancer is medullary thyroid cancer (MTC), papillary thyroid cancer (PTC) or thyroid gland medullary carcinoma; the colon cancer is colon adenocarcinoma; and/or the skin cancer is melanoma or cutaneous melanoma. G42. The use of embodiment G40 or G41, where the cancer is associated with a RET family PK aberration. G43. The use of any one of embodiments G40-G42, where the compound effectively inhibits or moderately inhibits a RET family PK. G44. The use of any one of embodiments G40-G43, where the compound is of any one of embodiments A1-A21 or optionally A16-A18.
G45. The use of any one of embodiments G1-G8, where the cancer is a liver cancer, breast cancer or AML. G46. The use of embodiment G45, where the cancer is associated with a PLK family PK aberration and optionally of a PLK4 family PK aberration. G47. The use of embodiments G45 or G46, where the compound effectively inhibits or moderately inhibits a PLK family PK, and optionally the compound is of any one of embodiments A1-A21 or optionally A19-A21. G48. The use of any one of embodiments G1-G47, where the medical condition is minimum residual disease (MRD). G49. The use of any one of embodiments G1-G5, where the medical condition is an inflammation condition, autoimmune condition and/or skin condition. G50. The use of embodiment G49, where: the inflammation condition is a chronic inflammation condition, senescent cell chronic inflammation condition or senescence-associated secretory phenotype condition; the autoimmune condition is atopic dermatitis, non-segmental vitiligo or rheumatoid arthritis; or the skin condition is atopic dermatitis, non-segmental vitiligo, psoriasis, plaque psoriasis, ultraviolet (UV) damaged skin, severely UV damaged skin, aged skin or severely aged skin. G51. The use of embodiment G49 or G50, where the skin condition is atopic dermatitis or non- segmental vitiligo. G52. The use of embodiment G49 or G50, where the medical condition is a psoriasis, optionally a moderate to severe psoriasis, optionally a moderate to severe plaque psoriasis, and/or optionally is treated in a subject who is a candidate for systemic therapy or phototherapy. G53. The use of any one of embodiments G49-G52, where the medical condition is associated with a TYK family PK aberration and optionally is associated with a TYK2 PK aberration. G54. The use of embodiment G53, where the compound effectively inhibits or moderately inhibits TYK2. G55. The use of embodiment G54, where the compound is of any one of embodiments A1-A21 or optionally A16-A18. Examples The examples below illustrate certain implementations and do not limit the technology.
Example 1: Preparation of ethyl 4-[[5-[(8-bromoquinazolin-2-yl)amino]-2-methyl- phenyl]carbamoyl]benzoate Described in this Example is a process for preparing ethyl 4-[[5-[(8-bromoquinazolin-2-yl)amino]-2- methyl-phenyl]carbamoyl]benzoate, an intermediate for preparing compound C1 in Table A, for example. Preparation of ethyl 4-[[5-(tert-butoxycarbonylamino)-2-methyl-phenyl]carbamoyl]benzoate
charged with 4-ethoxycarbonylbenzoic acid (1.42 g, 7.29 mmol). DMF (5 mL) was added and the mixture stirred until dissolution was complete. The vial was next charged with tert-butyl N-(3-amino-4-methyl-phenyl)carbamate (900 mg, 4.05 mmol) with rinsing using DMF (5 mL). TEA (1.0 mL, 7.29 mmol) was added. The vial was charged with EEDQ (1.80 g, 7.29 mmol) with rinsing using DMF (5 mL). The vial was sealed and stirred at room temperature (rt) for 24 hours (hr). LCMS showed the reaction was complete. The reaction was poured into excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), then water (1x), then 1N HCl (3x), and finally water. The organic phase was dried over MgSO4, filtered and evaporated to a pale yellow foam (1.192 grams). Attempted redissolution of the foam in EtOAc gives a white suspension of apparent solid. However, no filtration was carried out. The product was used without further purification. Preparation of ethyl 4-[(5-amino-2-methyl-phenyl)carbamoyl]benzoate
charged with a solution of ethyl 4-[[5-(tert-butoxycarbonylamino)-2- methyl-phenyl]carbamoyl]benzoate (325 mg, 0.82 mmol) in DCM (10 mL). The solution was treated with TFA (2 mL) at rt. The homogenous yellow reaction was stirred for 1 hr and sampled for LCMS. The reaction was complete. Toluene (10 mL) was added and the solution evaporated to a residue. The residue was partitioned between iPrOAc and saturated aqueous sodium bicarbonate (2x washes). The organic phase was dried over MgSO4, filtered and evaporated to a yellow oil (238 mg) which becomes a tacky, cream colored solid on standing. The material was used without further purification.
Preparation of ethyl 4-[[5-[(8-bromoquinazolin-2-yl)amino]-2-methyl-phenyl]carbamoyl]benzoate
vials were each charged with ethyl 4-[(5-amino-2-methyl- phenyl)carbamoyl]benzoate (156 mg each, 0.523 mmol). Each vial was then charged with 8-bromo- 2-chloro-quinazoline (637 mg, 2.615 mmol). EtOH (2.5 mL) was added to each and the combined solids were agitated using a pipette before sealing. The mixtures were placed in a 130°C aluminum block and vigorously stirred for 5 hours. The dark but transparent red-brown solutions were allowed to stand at rt over the weekend. A black precipitate was observed in each vial. The dark supernatants were sampled for LCMS. All three were identical, showing the complete consumption of the aniline. The three vials were rinsed with excess EtOH, then excess DCM, into a 250 mL round bottom (rb) flask, leaving behind some black insoluble material. The solution was evaporated to an orange- brown oil. IPA (10 mL) was added and the mixture heated until the residue dissolved. The dark solution was allowed to cool and stir at rt for 2 hr. The dark brown precipitated solid was recovered by filtration. The dark solid in the funnel was dissolved in excess DCM and filtered into a separate rb flask. The black solid remaining in the reaction vials was layered with excess DCM and stirred at rt for an hour, giving an orange-green supernatant. The operation was repeated three more times with the supernatants being collectively recovered. This third mixture was filtered, leaving behind a green solid in the funnel. There were four isolated materials. The DCM soluble material from the filter funnel, the first IPA filtrate, the DCM extract from the insoluble solids and the final solid left behind after all the solvent treatment. The DCM soluble material from the funnel yielded a dark brown semi-solid that solidified on standing (264 mg). The material was put through a solid phase extraction (SPE) process using 1 gram silica gel and 15 mL of 50:1 DCM/MeOH. This process yielded an orange solid (220 mg). The IPA filtrate yielded an orange-brown brittle foam (2.042 g). The material was put through a SPE process using 8 grams of silica gel and 80 mL of 50:1 DCM/MeOH. This process yielded an orange foam (1.037 g). The DCM filtrate from the insoluble solids yielded a yellow solid (122 mg) judged to be usable as is.
TLC of the SPE process materials showed removal of baseline material. The two materials were chromatographed on normal phase (0% to 5% MeOH/DCM). Some impure product was obtained (120 mg). The green insoluble material dissolved in DMSO. LCMS showed it was mostly product usable as is (155 mg). Total usable product isolated was 277 mg. Example 2: Preparation of C1 Described in this Example is a process for preparing compound C1 shown in Table A. Preparation of ethyl 4-[[5-[[8-(4-fluoro-2-isopropoxy-phenyl)quinazolin-2-yl]amino]-2-methyl- phenyl]carbamoyl]benzoate
vial with triangular stir vane was charged with (4-fluoro-2- isopropoxy-phenyl)boronic acid (15 mg, 0.074 mmol). A solution of ethyl 4-[[5-[(8-bromoquinazolin- 2-yl)amino]-2-methyl-phenyl]carbamoyl]benzoate (25 mg, 0.049 mmol; see Example 1) in dioxane (0.5 mL) was added followed by aqueous K3PO4 (0.074 mL, 2M, 0.15 mmol). Tetrakis(triphenylphosphine)palladium (13 mg, 0.011 mmol) was added and the vial sealed, then heated in an aluminum block (105°C) for 5 hours. LCMS indicated the reaction is complete with the formation of the desired product. The reaction was diluted with excess iPrOAc. MgSO4 was added and the mixture filtered and evaporated to a brown oil (50 mg). The oil was chromatographed on two 500 um pTLC plates using 2:1 H/EA. The major UV active spot/band was isolated (yellow solid, 7 mg). Preparation of 4-[[5-[[8-(4-fluoro-2-isopropoxy-phenyl)quinazolin-2-yl]amino]-2-methyl-
screw was a phenyl)quinazolin-2-yl]amino]-2-methyl-phenyl]carbamoyl]benzoate (7 mg, 0.012 mmol) in THF (0.5
mL). Solid LiOH (7 mg, 0.13 mmol) was added followed by water (20 μL, 1.11 mmol). The solution was stirred and heated in an aluminum block (85°C) for 16 hr. The reaction was diluted with excess iPrOAc and rendered acidic with aqueous 1N HCl. The organic was recovered, dried over MgSO4, filtered and evaporated to a yellow solid which was redissolved in EtOAc and transferred to a 20 mL scintillation vial. Pumping on high vacuum for 30 min gave a deep yellow oil (7 mg). Example 3: Preparation of C2 Described in this Example is a process for preparing compound C2 shown in Table A. Preparation of ethyl 4-((3-((tert-butoxycarbonyl)amino)-5-methylphenyl)carbamoyl)benzoate
with 4-ethoxycarbonylbenzoic acid (398 mg, 2.05 mmol). DMF (1.5 mL) was added and the mixture stirred until dissolution was complete. The vial was next charged with tert-butyl N-(3-amino-5-methyl-phenyl)carbamate (253 mg, 1.14 mmol) with rinsing using DMF (1.5 mL). TEA (284 mL, 2.05 mmol) was added. The vial was charged with EEDQ (507 mg, 2.05 mmol) with rinsing using DMF (1.5 mL). The vial was sealed and stirred at rt for 24 hr. LCMS shows the reaction is complete. The reaction was poured into excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), then water (1x), then 1N HCl (3x), and finally water. The organic layer was dried over MgSO4, filtered, and evaporated to a brown oil (169.5 mg). The material was used without further purification. Preparation of ethyl 4-((3-amino-5-methylphenyl)carbamoyl)benzoate
-5-methyl-phenyl]carbamoyl]benzoate (169.5 mg, 0.43 mmol) in DCM (1.70 mL) was treated with TFA (430 mL) at room temperature. The homogenous yellow reaction was stirred for 1 hr and sampled for LCMS. The reaction went to completion.
Toluene (10 mL) was added, and the solution evaporated to a residue. The residue was partitioned between iPrOAc and saturated aqueous sodium bicarbonate (2x washes). The organic layer was dried over MgSO4, filtered, and evaporated to a yellow oil (116 mg). The material was used without further purification. Preparation of ethyl 4-((3-((8-bromoquinazolin-2-yl)amino)-5-methylphenyl)carbamoyl)benzoate
were each charged with ethyl 4-((3-amino-5- methylphenyl)carbamoyl)benzoate (58 mg, 0.19 mmol; each batch). Each vial was then charged with 8-bromo-2-chloro-quinazoline (237 mg, 0.97 mmol; each batch). EtOH (3 mL each) was added, and the combined solids were agitated using a pipette before sealing. The mixtures were heated to 130°C in an aluminum block, and vigorously stirred for 5 hours. The two vials were rinsed with excess EtOH, then excess DCM, into a 250 mL round-bottomed flask. The solution was evaporated to an orange-brown oil. IPA (10 mL) was added, and the mixture heated until the residue dissolved. The dark solution was allowed to cool and stir at room temperature for 12 hr. The dark brown precipitated solid was recovered by filtration (83.1 mg). The material was used without further purification. Preparation of ethyl 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-5-
4-fluoro-2- isopropoxy-phenyl)boronic acid (23.5 mg, 0.118 mmol). A solution of ethyl 4-((3-((8-(4-fluoro-2- isopropoxyphenyl)quinazolin-2-yl)amino)-5-methylphenyl)carbamoyl)benzoate (40 mg, 0.079 mmol) in dioxane (790 mL) was added followed by aqueous K3PO4 (120 mL, 2M, 0.237 mmol). Tetrakis(triphenylphosphine)palladium (18.3 mg, 0.015 mmol) was added, the vial sealed, then heated in an aluminum block (105°C) for 16 hours.
LCMS indicated the reaction went to completion. The reaction was diluted with excess iPrOAc. MgSO4 was added, the mixture was filtered, and evaporated to a yellow oil. The oil was purified by preparative thin layer chromatography on two 500 mm pTLC plates using 40:1 DCM:MeOH. The major UV-active band was isolated (yellow solid, 18 mg). Preparation of 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-5- benzoic acid
with a solution of ethyl 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-5-methylphenyl)carbamoyl)benzoate (33 mg, 0.060 mmol) in THF (1 mL). Water (20 uL, 1.11 mmol) was added followed by LiOH hydrate (25 mg, 0.601 mmol). The vial was sealed and heated with stirring in an aluminum block (85 °C) for 16 hr. Reaction was incomplete upon analysis by LCMS. Additional LiOH monohydrate (25 mg, 0.601 mmol) was added. The reaction was stirred in an aluminum block (85°C) for 16 hr. The reaction was diluted with excess iPrOAc and rendered acidic with aqueous 1N HCl. The organic phase was recovered, dried over MgSO4, filtered, and evaporated to a yellow solid. The compound was purified by preparative thin layer chromatography on two 500 mm pTLC plates using 40:1 DCM:MeOH. The plates required three consecutive runs to achieve separation. The major UV-active band was isolated (pale yellow solid, 3 mg). Example 4: Preparation of C3 Described in this Example is a process for preparing compound C3 shown in Table A. Preparation of ethyl 4-((5-((tert-butoxycarbonyl)amino)-2-methoxyphenyl)carbamoyl)benzoate
was mg, . DMF (2.8 mL) was added and the mixture stirred until dissolution was complete. The vial was next
charged with tert-butyl N-(3-amino-4-methoxy-phenyl)carbamate (500 mg, 2.10 mmol) with rinsing using DMF (2.8 mL). TEA (524 mL, 3.78 mmol) was added. The vial was charged with EEDQ (934 mg, 3.78 mmol) with rinsing using DMF (2.8 mL). The vial was sealed and stirred at rt for 24 hr. LCMS showed the reaction was complete. The reaction was poured into excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), then water (1x), then 1N HCl (3x), and finally water. The organic layer was dried over MgSO4, filtered, and evaporated to a yellow oil (304 mg). The material was used without further purification. Preparation of ethyl 4-((5-amino-2-methoxyphenyl)carbamoyl)benzoate
amino)-2-methoxyphenyl)carbamoyl)benzoate (304 mg, 0.73 mmol) in DCM (2.9 mL) was treated with TFA (740 mL) at rt. The homogenous yellow reaction was stirred for 1 hr and sampled for LCMS. The reaction went to completion. Toluene (10 mL) was added and the solution evaporated to a residue. The residue was partitioned between iPrOAc and saturated aqueous sodium bicarbonate (2x washes). The organic layer was dried over MgSO4, filtered, and evaporated to a yellow oil (224 mg). The material was used without further purification. Preparation of ethyl 4-((5-((8-bromoquinazolin-2-yl)amino)-2-methoxyphenyl)carbamoyl)benzoate
were each charged with ethyl 4-((5-amino-2- methoxyphenyl)carbamoyl)benzoate (112 mg, 0.375 mmol; each batch). Each vial was then charged with 8-bromo-2-chloro-quinazoline (433 mg, 1.78 mmol; each batch). EtOH (2.5 mL each) was added, and the combined solids were agitated using a pipette before sealing. The mixtures were placed in a 130°C aluminum block and vigorously stirred for 5 hours. The two vials were rinsed with excess EtOH, then excess DCM, into a 250 mL round-bottomed (rb) flask. The solution was evaporated to an orange-brown oil. IPA (10 mL) was added and the mixture
heated until the residue dissolved. The dark solution was allowed to cool and stir at room temperature for 12 hr. The dark brown precipitated solid was recovered by filtration (126 mg). The material was used without further purification. Preparation of ethyl 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoate
stir vane was charged with 4-fluoro-2- isopropoxy-phenyl)boronic acid (22.8 mg, 0.115 mmol). A solution of ethyl 4-((5-((8- bromoquinazolin-2-yl)amino)-2-methoxyphenyl)carbamoyl)benzoate (40 mg, 0.076 mmol) in dioxane (770 mL) was added followed by aqueous K3PO4 (114 mL, 2M, 0.228 mmol). Tetrakis(triphenylphosphine)palladium (17.7 mg, 0.015 mmol) was added, the vial sealed, then heated in an aluminum block (105°C) for 16 hours. LCMS indicated the reaction went to completion. The reaction was diluted with excess iPrOAc. MgSO4 was added, the mixture was filtered, and evaporated to a yellow oil. The oil was purified by preparative thin layer chromatography on two 500 mm pTLC plates using 40:1 DCM:MeOH. The major UV-active band was isolated (yellow solid, 16.3 mg). Preparation of 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2-
– with a solution of ethyl 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoate (16.3 mg, 0.027 mmol) in THF (1 mL). Water (20 uL, 1.11
mmol) was added followed by LiOH monohydrate (25 mg, 0.601 mmol). The vial was sealed and heated with stirring in an aluminum block (85°C) for 16 hr. The yellow solution with a suspended bright yellow solid was diluted with excess iPrOAc and washed with excess 1N HCl. The yellow solid did not dissolve. The clear aqueous layer was separated, and the organic layer washed once with water. The iPrOAc/solid mixture was evaporated to dryness leaving a bright yellow solid (27 mg). The compound was purified by preparative thin layer chromatography on two 500 mm pTLC plates using 40:1 DCM:MeOH. The major UV-active band was isolated (yellow solid, 6.3 mg). Example 5: Preparation of C4 Described in this Example is a process for preparing compound C4 shown in Table A. Preparation of ethyl 4-((5-((8-(2-isopropylphenyl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoate
with triangular stir vane was charged with ethyl 4-[[5-[(8- bromo-2-naphthyl)amino]-2-methyl-phenyl]carbamoyl]benzoate (64 mg, 0.13 mmol). A turbid solution of ((2-isopropylphenyl)boronic acid (31 mg, 0.19 mmol) in dioxane (1 mL) was added. The solid was suspended in the mixture by stirring for a minute. Aqueous K3PO4 (190 μL, 2.0 M, 0.38 mmol) was added, followed by tetrakis(triphenylphoshine) palladium (29 mg, 0.025 mmol). The vessel was sealed and the mixture heated in an aluminum block (105°C) for 5 hours. LCMS indicated the reaction was complete with the formation of the desired product. The reaction was diluted with excess iPrOAc. MgSO4 was added and the mixture filtered and evaporated to a brown oil (121 mg). The oil was chromatographed by preparative TLC using 40:1 DCM/MeOH. The major UV active band was isolated (42 mg). The product was used without further purification. Preparation of 4-((5-((8-(2-isopropylphenyl)quinazolin-2-yl)amino)-2-
A 0.5 - 2.0 mL tapered microwave vial with triangular stir vane was charged with a suspension of ethyl 4-[[5-[[8-(2-isopropylphenyl)quinazolin-2-yl]amino]-2-methyl-phenyl]carbamoyl]benzoate (52 mg, 0.095 mmol) in THF (1 mL). Water (20 uL, 1.11 mmol) was added followed by LiOH hydrate (40 mg, 0.95 mmol). The vial was sealed and heated in an aluminum block (85°C) overnight. The dark suspension of solid was diluted with excess iPrOAc and treated with excess 1N HCl. Most of the material dissolved leaving a yellow organic and a clear aqueous with a small amount of suspended black flocculent material. The aqueous phase was drawn off and the organic phase dried over MgSO4. The mixture was filtered and evaporated to a yellow/orange semisolid (45 mg). LCMS showed the reaction was complete and that the product is of acceptable purity. Example 6: Preparation of C5 Described in this Example is a process for preparing compound C5 shown in Table A. Preparation of ethyl 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2-
with (2- isobutylpyrazol-3-yl)boronic acid (19.3 mg, 0.115 mmol). A solution of ethyl 4-((5-((8- bromoquinazolin-2-yl)amino)-2-methoxyphenyl)carbamoyl)benzoate (40 mg, 0.076 mmol) in dioxane (770 mL) was added followed by aqueous K3PO4 (114 mL, 2M, 0.228 mmol). Tetrakis(triphenylphosphine)palladium (17.7 mg, 0.015 mmol) was added, the vial sealed, then heated in an aluminum block (105°C) for 5 hours. LCMS indicated the reaction went to completion. The reaction was diluted with excess iPrOAc. MgSO4 was added, the mixture was filtered, and evaporated to a yellow oil. The oil was purified by preparative thin layer chromatography on two 500 mm pTLC plates using 40:1 DCM:MeOH. The major UV-active band was isolated (yellow solid, 9.1 mg).
Preparation of 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid (C5) N HO2C N
stir vane was charged with a solution of ethyl 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2-methoxyphenyl)carbamoyl)benzoate (9.1 mg, 0.016 mmol) in THF (640 mL). Water (20 mL, 1.11 mmol) was added followed by LiOH monohydrate (6.7 mg, 0.161 mmol). The vial was sealed and heated with stirring in an aluminum block (85°C) for 16 hr. The yellow solution with a suspended bright yellow solid was diluted with excess iPrOAc and washed with excess 1N HCl. The yellow solid does not dissolve. The clear aqueous layer was separated, and the organic layer washed once with water. The iPrOAc/solid mixture was evaporated to dryness leaving a bright yellow solid. No further purification was required (8 mg). Example 7: Preparation of C6 Described in this Example is a process for preparing compound C6 shown in Table A. Preparation of ethyl 4-[[5-[[8-(2-isobutylpyrazol-3-yl)-2-naphthyl]amino]-2-methyl- phenyl]carbamoyl]benzoate
with triangular stir vane was charged with ethyl 4-[[5-[(8- bromo-2-naphthyl)amino]-2-methyl-phenyl]carbamoyl]benzoate (81 mg, 0.161 mmol). A turbid solution of (2-isobutylpyrazol-3-yl)boronic acid (41 mg, 0.241 mmol mmol) in dioxane (1 mL) was added. The solid was suspended in the mixture by stirring for a minute. Aqueous K3PO4 (240 μL, 2.0 M, 0.483 mmol ) was added followed by tetrakis(triphenylphoshine) palladium (37 mg, 0.032 mmol). The vessel was sealed and the mixture heated in an aluminum block (105°C) for 5 hr. LCMS shows the desired product is present. The reaction was diluted with excess iPrOAc and dried over MgSO4. Filtration and evaporation afforded a dark residue (132 mg). The residue was
dissolved in IPA at reflux (6 mL), then allowed to stir at rt for 2 hr. The mixture was filtered and the recovered solid allowed to stand under lyophilizer vacuum in the filter funnel for 1 hr. LCMS showed the yellow solid was not much different from the reaction (33 mg). The solid was chromatographed on a 500 uM prep TLC plate (40:1 DCM/MeOH). The major band was collected to afford the product (light yellow solid, 31 mg). Preparation of 4-((5-((8-(1-isobutyl-1H-pyrazol-5-yl)quinazolin-2-yl)amino)-2- methylphenyl)carbamoyl)benzoic acid (C6)
with triangular stir vane was charged with a solution of ethyl 4-[[5-[[8-(2-isobutylpyrazol-3-yl)quinazolin-2-yl]amino]-2-methyl-phenyl]carbamoyl]benzoate (33 mg, 0.060 mmol) in THF (1 mL). Water (20 uL, 1.11 mmol) was added followed by LiOH hydrate (25 mg, 0.601 mmol). The vial was sealed and heated with stirring in an aluminum block (85°C) for 16 hr. The yellow solution with a suspended bright yellow solid was diluted with excess iPrOAc and washed with excess 1N HCl. The yellow solid did not dissolve. The clear aqueous phase was drawn off and the organic phase washed once with water. The aqueous phase was drawn off. The iPrOAc/solid mixture was evaporated to dryness leaving a bright yellow solid (27 mg). LCMS showed the desired product along with a single major impurity. The solid was dissolved in hot MeOH and treated with 0.5 mL of 1N HCl. The turbid yellow solution was evaporated to dryness, yielding a yellow solid. The solid was exhaustively extracted with DCM with filtration of the DCM extracts. The solid was then dissolved in excess EtOH. The EtOH was used to rinse down the filter funnel. The filtrate was collected and evaporated to a yellow solid (32 mg). LCMS still showed the presence of the impurity at 4.27 min in the same abundance as before. The material was chromatographed on a 500 μm pTLC plate (20:1:0.1 DCM/MeOH/AcOH). Two bands of material were isolated: a more mobile narrow band (5 mg) and a less mobile broad band just above the baseline (17 mg). Each of the materials was suspended separately in CHCl3, brought to a boil, allowed to cool to rt and stand for 3 hr, each material leaving a white residue deposited on the side of their respective vials.
The supernatant of each was sampled for LCMS. The supernatant from the 17 mg batch showed the presence of the desired product in acceptable purity. The liquid was carefully drawn off with a microliter syringe and evaporated to a light yellow solid (C6, 2 mg). The rest of the material was combined, filtered and evaporated to a light yellow solid (6 mg). Example 8: Preparation of C7 Described in this Example is a process for preparing compound C7 shown in Table A. Preparation of ethyl 4-((3-((tert-butoxycarbonyl)amino)phenyl)carbamoyl)benzoate
1.009 mmol) followed by tert-butyl N-(3-aminophenyl)carbamate (116 mg, 0.557 mmol). DMF (2 mL) was added and the mixture stirred until dissolution was complete, giving an opaque black solution. TEA (140 μL, 1.003 mmol) was added followed by EEDQ (248 mg, 1.009 mmol). The dark solution was stirred at rt overnight. LCMS showed a major product with the desired mass. The reaction was diluted with excess iPrOAc and washed with saturated aqueous sodium bicarbonate (3x), water, 1N HCl (3x) and then water. The brown organic was dried over MgSO4, filtered and evaporated to a dark oil that became a tan solid upon standing under high vacuum (116 mg). The material was used without further purification. Preparation of ethyl 4-((3-aminophenyl)carbamoyl)benzoate
(tert-butoxycarbonylamino)-phenyl]carbamoyl]benzoate (116 mg, 0.302 mmol) in DCM (3 mL) was treated with TFA (0.6 mL) at rt. The homogenous yellow reaction was stirred for 1 hr and sampled for LCMS. The reaction was determined as being complete. Toluene (4 mL) was added and the solution evaporated to a residue. The residue was partitioned between iPrOAc and saturated aqueous sodium bicarbonate (2x washes). The organic phase was dried over MgSO4, filtered and evaporated to a yellow oil which became a tacky, cream colored solid on standing. The material was used without further purification (61 mg).
Preparation of ethyl 4-((3-((8-bromoquinazolin-2-yl)amino)phenyl)carbamoyl)benzoate
vial was charged with a solution of ethyl 4-[3- aminophenyl)carbamoyl]benzoate (61 mg, 0.21mmol) in EtOH (2 mL). Solid 8-bromo-2-chloro- quinazoline (261 mg, 1.07 mmol) was added. The solution was sealed in a vial and heated to 125°C in an aluminum block for 5 hours. LCMS showed that all of the aniline is consumed and the desired product was present. Upon cooling the solution a green suspension was formed. It was rinsed with excess EtOH, and then with excess DCM into a 250 mL rb flask, which left behind a dark insoluble material. The solution was evaporated to an orange oil. IPA (3 mL) was added and the mixture was heated up to dissolve the material. Upon cooling and stirring at rt for 2 hr, the precipitated solid was recovered by filtration. The solid was dissolved in excess DCM and filtered into a separate rb flask. The solid left in the microwavable vial was layered with excess DCM and stirred at rt for a hour yielding an orange supernatant. This operation was repeated three more times with the supernatants being collectively recovered. The DCM solutions were combined to afford the product (14 mg). Preparation of ethyl 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2- yl)amino)phenyl)carbamoyl)benzoate
vial with triangular stir vane was charged with (4-fluoro-2- isopropoxyphenyl)boronic acid (8.43 mg, 0.042 mmol). A solution of ethyl 4-[[3-[(8- bromoquinazolin-2-yl)amino]phenyl]carbamoyl]benzoate (13.8 mg, 0.028 mmol) in dioxane (0.06 mL) was added followed by aqueous K3PO4 (0.042 mL, 2M, 0.084 mmol). Tetrakis(triphenylphosphine)palladium (7.45 mg, 0.006 mmol) was added and the vial sealed, then heated in an aluminum block (105°C) for 5 hours.
LCMS indicated the reaction was complete with the formation of the desired product. The reaction was diluted with excess iPrOAc. MgSO4 was added and the mixture filtered and evaporated to a brown oil. The oil was chromatographed on a 500 µm pTLC plate using 2:1 Hexane/EtOAc. The major UV-active band was isolated (5 mg). Preparation of 4-((3-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2- benzoic acid
[[3-[[8-(4-fluoro-3-isopropoxy- phenyl)quinazolin-2-yl]amino]phenyl]carbamoyl]benzoate (5 mg, 0.008 mmol). THF (0.3 mL) was added followed by water (24 μL, 1.33 mmol). LiOH monohydrate (3.5 mg, 0.08 mmol) was added and the vial sealed, then heated with stirring in an aluminum block (85°C) for 6 hr. A white precipitate was observed. The reaction was cooled to rt, diluted with excess iPrOAc and acidified with 1N HCl until all solids dissolved. The clear aqueous was removed and the yellow organic dried over MgSO4, filtered and evaporated to a yellow semisolid (24 mg). LCMS shows that the hydrolysis is complete. The solid was chromatographed on a 500 µm pTLC plate using 40:1 DCM/MeOH. The major UV-active band near the baseline was isolated affording the desired product (5 mg). Example 9: Protein Kinase Inhibition Assays and Results This Example describes a cell-free assay utilized to identify candidate compounds that bind to and inhibit protein kinase (PK) and PK variants. One assay is referred to as a "Z´-LYTE assay" and is an example of a labeled peptide cleavage assay. The fluorescence-based assay relies on the differential sensitivity of a small, dual-end-labelled peptide to cleavage by a protease, dependent on the phosphorylation state of the peptide (FIG.1). The peptide substrate is end-labelled with two distinct fluorophores that comprise a Fluorescence Resonance Energy Transfer (FRET) pair. In the absence of inhibitor, the kinase transfers the gamma-phosphate from ATP to the single, unique tyrosine, serine or threonine in the synthetic FRET peptide. The reaction conditions are titrated such that 10-40% of the peptide substrate is phosphorylated. In a second reaction, a site- specific protease that only recognizes and cleaves the non-phosphorylated FRET peptide is added. Cleavage interferes with FRET between the donor (i.e., coumarin) and the acceptor (i.e.,
fluorescein) fluorophores on the FRET-peptide substrate, unlike the phosphorylated, uncleaved peptide. To quantitate phosphorylation activity of the kinase, a ratiometric method is used, which is based on the ratio (Emission Ratio (ER)) of donor emission to acceptor emission after excitation of the donor coumarin at 400 nm, using the formula: ER = Coumarin Emission (445 nm)/Fluorescein Emission (520 nm). In this approach, both cleaved and uncleaved FRET-peptides contribute to the two fluorescence signals and hence to the ER. Based on the ER, the extent of phosphorylation of the FRET-peptide can be calculated. If the FRET-peptide is phosphorylated (i.e., no or less kinase-mediated phosphorylation inhibition), the ER is relatively low, but if kinase-mediated phosphorylation is inhibited, the ER is relatively high. This ratiometric approach to quantitating reaction progress virtually eliminates well-to-well variations in FRET-peptide concentration and signal intensities, leading to very high Z’-factor values (> 0.7; World Wide Web URL en.wikipedia.org/wiki/Z-factor) at a low percent phosphorylation. Assay regents and conditions are described for an ABL1 PK assay, and are described thereafter for other PK assays. Assay Conditions Test compounds The Test Compounds are screened in 1% DMSO (final) in the well. For 10-point titrations, 3-fold serial dilutions are conducted from a relatively high starting concentration (e.g., 10 micromolar (μM)), considered to be much greater than an IC50 of likely pharmaceutical value. ABL1 PK assay reagents All Peptide/Kinase Mixtures are diluted to a 2X working concentration in the appropriate Kinase Buffer. The 2X ABL1 polypeptide/ Tyr 02 substrate peptide mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 0.3 - 1.2 ng ABL1 (or 1.36 – 6 ng ABL1(T315I)) and 2 μM Tyr 02 in 50 mM HEPES, pH 7.5, 0.01% BRIJ- 35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. The ABL1(wt) polypeptide utilized for the assay described in this Example was the "isoahABL1(wt)" polypeptide described herein (SEQ ID NO:4), which is referred to as "ABL1" in Table 1 and "ABL1(wt)" or "WT" in Table 3 of this Example. The ABL1 variant polypeptides utilized contained the same polypeptide as the "isoahABL1(wt)" polypeptide except that each contained one corresponding amino acid substitution chosen from E255K, F317I, F317L, G250E, T315I or Y253F. The ABL1 variant polypeptides are referred to as
"ABL1 E255K," "ABL1 F317I," "ABL1 F317L," "ABL1 G250E," "ABL1 T315I" and "ABL1 Y253F" in Table 1 of this Example according to the corresponding amino acid substitution contained and are referred to in Table 3 of this Example according to the corresponding amino acid substitution contained. All ATP Solutions are diluted to a 4X working concentration in Kinase Buffer (50 mM HEPES, pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA). The ATP Km apparent (Km app) is previously determined using a Z´-LYTE assay. The following Table 1 in this Example shows IC50 values for particular inhibitors of phosphorylation activity for ABL1(wt) polypeptide and ABL1 variant polypeptides. Table 1
The Development Reagent (i.e., with protease) is diluted in Development Buffer. Assay Protocol Bar-coded Corning, low volume NBS, black 384-well plate (Corning Cat. #4514) 1.100 nL – 100X Test Compound in 100% DMSO 2.2.4 μL – Kinase buffer 3.5 μL – 2X Peptide/Kinase Mixture 4.2.5 μL – 4X ATP Solution 5.30-second plate shake 6.60-minute Kinase Reaction incubation at room temperature 7.5 μL – Development Reagent Solution 8.30-second plate shake 9.60-minute Development Reaction incubation at room temperature 10. Read on fluorescence plate reader and analyze the data
Z′-LYTE Assay Controls The following controls are made for each individual kinase and are located on the same plate as the kinase. 0% Phosphorylation Control (100% Inhibition Control) The maximum Emission Ratio is established by the 0% Phosphorylation Control (100% Inhibition Control), which contains no ATP and therefore exhibits no kinase activity. This control yields 100% cleaved peptide in the Development Reaction. 100% Phosphorylation Control The 100% Phosphorylation Control, which contains a synthetically phosphorylated peptide of the same sequence as the peptide substrate, is designed to allow for the calculation of percent phosphorylation. This control yields a very low percentage of cleaved peptide in the Development Reaction. The 0% Phosphorylation and 100% Phosphorylation Controls allow one to calculate the percent Phosphorylation achieved in a specific reaction well. Control wells do not include any kinase inhibitors. 0% Inhibition Control The minimum Emission Ratio in a screen is established by the 0% Inhibition Control, which contains active kinase. This control is designed to produce a 10–50% phosphorylated peptide in the Kinase Reaction. Cascade assays may produce up to 70% phosphorylated peptide. Known Inhibitor A known inhibitor control standard curve, 10-point titration, is run for each individual kinase on the same plate as the kinase to ensure the kinase is inhibited within an expected IC50 range previously determined. The following controls are prepared for each concentration of Test Compound assayed: Development Reaction Interference The Development Reaction Interference is established by comparing the Test Compound Control wells that do not contain ATP versus the 0% Phosphorylation Control (which does not contain the Test Compound). The expected value for a non-interfering compound should be 100%. Any value outside of 90% to 110% is flagged. Test Compound Fluorescence Interference
The Test Compound Fluorescence Interference is determined by comparing the Test Compound Control wells that do not contain the Kinase/Peptide Mixture (zero peptide control) versus the 0% Inhibition Control. The expected value for a non-fluorescence compound should be 0%. Any value > 20% is flagged.
Graphing Software SelectScreen Kinase Profiling Service uses XLfit from IDBS. The dose response curve is curve fit to model number 205 (sigmoidal dose-response model). If the bottom of the curve does not fit between -20% & 20% inhibition, it is set to 0% inhibition. If the top of the curve does not fit between 70% and 130% inhibition, it is set to 100% inhibition. Z′-LYTE Data Analysis The equations shown in the following Table 2 of this Example are used for each set of data points: Table 2
The description of the assay in this Example is excerpted from (Z’LYTE™ Screening Protocol and Assay Conditions (rev 29 Jan 2021)).
Other PK assays Assays for PKs other than ABL1 generally followed the ABL1 PK assay format described previously in this Example, although the identity of Substrates and Inhibitor and the amounts of Kinase Enzyme, ATP inhibitors and Dilution Reagent A added were optimized for each PK, as summarized hereafter. AURKA (Aurora A) and AURKB (Aurora B): The 2X AURKA (Aurora A) / Ser/Thr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 0.75 - 3 ng AURKA (Aurora A) or 3.5 - 18 ng AURKB (Aurora B) and 2 μM Ser/Thr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:4096 dilution of Development Reagent A is added. AURKC (Aurora C): The 2X AURKC (Aurora C) / Ser/Thr 19 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 2 - 20 ng AURKC (Aurora C) and 2 μM Ser/Thr 19 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:256 dilution of Development Reagent A is added. BTK, BMX and ITK: The 2X BTK / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 0.52 - 3.36 ng BTK, or 2.5 - 10 ng BMX, or 4.69 - 60 ng ITK, and 2 μM Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent B is added. JAK1, JAK2 and JAK3: The 2X JAK1 / Tyr 06 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3. The final 10 μL Kinase Reaction contains 22.9 - 91.5 ng JAK1, or 0.12 - 0.5 ng JAK2, 1.75 – 9 ng JAK2 JH1-JH2-V617F, or 0.5 - 2.7 ng JAK3 and 2 μM Tyr 06 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. EPHA1 and EPHB1: The 2X EPHA1 / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase. The reaction contains 3.12 - 38.6 ng EPHA1 (or 1.2 – 4.8 ng EPHA8, or 2.4 – 10 ng EPHB1, or 0.55 – 2.86 ng EPHB1) and 2 μM Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. EPHA2: The 2X EPHA2 / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 2.1 - 8.8 ng EPHA2 (or 1.2 – 7.5
ng EPHA5) and 2 μM Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent B is added. TRKA (NTRK1) and TRKC (NTRK3): The 2X NTRK1 (TRKA) / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 6 - 24 ng NTRK1 (TRKA) or 2.7 – 30 ng NTRK3 (TRKC), and 2 μM Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent B is added. TRKB (NTRK2): The 2X NTRK2 (TRKB) / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 4 mM MnCl2, 1 mM EGTA, 2 mM DTT. The final 10 μL Kinase Reaction contains 0.34 - 4 ng NTRK2 (TRKB) and 2 μM Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 2 mM MnCl2, 1 mM EGTA, 1 mM DTT. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent B is added. ROS1: The 2X ROS1 / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 3 - 12 ng ROS1 and 2 μM Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent B is added. TNK1: The 2X TNK1 / Ser/Thr 13 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3. The final 10 μL Kinase Reaction contains 15 - 60 ng TNK1 and 2 μM Ser/Thr 13 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:1024 dilution of Development Reagent A is added. TXK: The 2X TXK / Tyr 06 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 4.75 - 19 ng TXK and 2 μM Tyr 06 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. TYK2: The 2X TYK2 / Tyr 03 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3. The final 10 μL Kinase Reaction contains 3.75 - 15 ng TYK2 and 2 μM Tyr 03 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3. After the 1 hour Kinase Reaction incubation, 5 μL of a 1:4096 dilution of Development Reagent A is added. RET: The 2X RET / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 0.49 - 3.64 ng RET (or 0.52 – 4.74
ng RET-V804L or 0.86 – 6.16 ng RET-Y791F) and 2 μM Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. RET-A883F: The 2X RET A883F / Tyr 04 mixture is prepared in 50 mM HEPES pH 6.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.02% NaN3. The final 10 μL Kinase Reaction contains 1.02 - 6.74 ng RET-A883F (or 3 – 20 ng RET-V804L) and 2 μM Tyr 04 in 50 mM HEPES pH 7.0, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA, 0.01% NaN3. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:64 dilution of Development Reagent B is added. RET-S891A: The 2X RET S891A / Tyr 06 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 0.3 - 1.4 ng RET- S891A and 2 μM Tyr 06 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. ABL2 (Arg): The 2X ABL2 (Arg) / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ- 35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 0.42 - 3.13 ng ABL2 (Arg) and 2 μM Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. PTK2B (FAK2): The 2X PTK2B (FAK2) / Tyr 01 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MnCl2, 1 mM EGTA, 2 mM DTT, 0.02% NaN3. The final 10 μL Kinase Reaction contains 5.26 - 34.8 ng PTK2B (FAK2) and 2 μM Tyr 01 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 5 mM MgCl2, 5 mM MnCl2, 1 mM EGTA, 1 mM DTT, 0.01% NaN3. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent B is added. SRC, SRC-N1: The 2X SRC / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction consists of 5 - 20 ng SRC (or 1 – 4.9 ng SRC-N1) and 2 μM Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added. LCK: The 2X LCK / Tyr 02 mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction consists of 8 - 33 ng LCK and 2 μM Tyr 02 in 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of a 1:128 dilution of Development Reagent A is added.
The following Table 3 in this Example shows IC50 values for particular inhibitors of phosphorylation activity for PKs other than ABL1. Table 3 Z’-LYTE ATP ATP Assay Bin Ctl Inhibitor IC50 (nM) Substrate Km app (uM) (uM)
Z’-LYTE ATP ATP Assay Ctl Inhibitor IC50 (nM) Substrate Km app (uM) Bin (uM) Eu
Kinase Binding Assay, which is an example of a fluorescence displacement assay. In this case, an Alexa Fluor™-conjugated “tracer”, or control binding ligand, is added to an epitope-tagged target protein in solution. At the same time, an Eu (europium)-labeled anti-tag antibody is added, resulting in a high degree of Fluorescence resonance energy transfer (FRET), whereas displacement of the tracer with a kinase inhibitor leads to a reduction of FRET. For more experimental details, see “LanthaScreen™ Eu Kinase Binding Assay Screening Protocol and Assay Conditions” (Revised 29 Jan-2021) from SelectScreen™ Biochemical Kinase Profiling Service (World Wide Web address URL thermofisher.com/selectscreen). For example, TEC, IRAK3, PLK4, RET-G691S, RET-V804M, RET-M918T, TNK2 (ACK), DDR2- N456S and DDR2-T654M PKs were assayed using the Lantha Screen. The TEC PK concentration was 1 nM using an Eu-anti-His antibody (2 nM) and Tracer 178 at 1 nM (Kd = 1 nM). The control inhibitor for the TEC PK was dasatinib (IC50 = 72.6 nM). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA.
The IRAK3 kinase concentration was 1 nM using an Eu-anti-GST antibody (2 nM) and Tracer 236 at 5 nM (Kd = 2.7 nM). The control inhibitor was Staurosporine (IC50 = 0.351 nM). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2 and 1 mM EGTA. The PLK4 kinase concentration was 1 nM using an Eu-anti-GST antibody (2 nM) and Tracer 236 at 1 nM (Kd = 1.7 nM). The control inhibitor was Staurosporine (IC50 = 1.46 nM). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2 and 1 mM EGTA. The RET-G691S, -V804M, and -M918T kinase concentrations were 5, 2.5, and 20 nM, respectively using an Eu-anti-GST antibody (2 nM) and Tracer 236 at 10, 5, and 10 nM, respectively (Kds = 12, 2.2, and 11 nM, respectively). The control inhibitor was staurosporine (IC50 = 3.18, 1.02, and 3.8 nM, respectively). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The TNK2 (ACK) kinase concentration was 5 nM using an Eu-anti-GST antibody (2 nM) and Tracer 236 at 30 nM (Kd = 23 nM). The control inhibitor was Staurosporine (IC50 = 4.07 nM). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The DDR2-N456S kinase concentration was 1 nM using an Eu-anti-GST antibody (2 nM) and Tracer 236 at 1 nM (Kd = 1.8 nM). The control inhibitor was Staurosporine (IC50 = 0.134 nM). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. The DDR2-T654M kinase concentration was 20 nM using an Eu-anti-GST antibody (2 nM) and Tracer 178 at 100 nM (Kd = 166 nM). The control inhibitor was Dasatinib (IC50 = 139 nM). The Buffer was 50 mM HEPES pH 7.5, 0.01% BRIJ-35, 10 mM MgCl2, 1 mM EGTA. For IRAK1, a different type of assay was conducted, known as an Adapta™ Assay based on ADP formation from ATP hydrolysis. It can be used to measure any type of ATP hydrolysis, including the intrinsic ATPase activity of kinases. In this assay, the substrate is water and not a peptide. This assay is described in Kashem, MA et al. (2007) J. Biomol. Screen.12:70-83. For IRAK1 assay, the 2X IRAK1 / Histone H3 (1-20) peptide mixture is prepared in 50 mM HEPES pH 7.5, 0.01% BRIJ- 35, 10 mM MgCl2, 1 mM EGTA. The final 10 μL Kinase Reaction contains 3.5 - 30.5 ng IRAK1 and 100 μM Histone H3 (1-20) peptide in 32.5 mM HEPES pH 7.5, 0.005% BRIJ-35, 5 mM MgCl2, 0.5 mM EGTA. After the 1-hour Kinase Reaction incubation, 5 μL of Detection Mix is added. For additional details, see “Adapta™ Screening Protocol and Assay Conditions” (Revised 29 Jan-2021) from SelectScreen™ Biochemical Kinase Profiling Service (World Wide Web URL thermofisher.com/selectscreen). The following Table 4 in this Example shows public database accession numbers for PK polypeptides (“NP” and “AA” prefix accession numbers in the World Wide Web URL ncbi.nlm.nih.gov/protein/ database and “P” prefix accession numbers in the World Wide Web URL
uniprot.org/uniprotkb/ database), the epitope tag attached and the purity of the PK utilized in each assay. Table 4 PTK* Accession number* Epitope Purity (SDS PAGE) ABL1(wt) NP 0051482 6xHi 80%
PTK* Accession number* Epitope Purity (SDS PAGE) PLK4(wt)^ NP 055079.3 GST 70% says is
y q p p yp p y ponding accession number; ^ LanthaScreen™ Eu Kinase Binding Assay was utilized; ^^ LanthaScreen™ Eu Kinase Binding Assay was utilized for certain RET variants; ^^^ Adapta™ Assay was utilized; Z’LYTE™ assay utilized for PKs listed in Table 4 not designated by ^, ^^ or ^^^; “GST” is glutathione S-transferase conjugate and “6xHis” is a peptide conjugate consisting of six consecutive histidine amino acids. Assay Results The following Table 5 reports IC50 values obtained for test compounds using the assay described in this Example. The IC50 value for each test compound measured for ABL1(wt) and ABL1 variants is reported in nanomolar (nM) units. ABL1 variants were ABL1(T315I), ABL1(G250E), ABL1(Y253F), ABL1(E255K) and ABL1(F317L), which are referred to in the following Table 5 of this Example by the amino acid substitution in each ABL1 variant. Certain IC50 values are referenced from publications cited as shown. Several clinical inhibitors were analyzed and are referred to in Table 5 of this Example as "ClinIn1" to "ClinIn6." Test compound C1 is described in Example 2 herein. Test compounds "CompA" and "CompB" are comparative test compounds identified by the library screening process that identified compound C1.
Table 5 Test ABL1(wt) G250E Y253F E255K T315I F317L Ratio Compound WT:T315I
repore n e ae e a., . n. ncoogy: : . . . . ( ) #reported in Manley et al., Leukemia Research 98:106458 (2020) ^reported in O’Hare et al., Cancer Cell 16, 401–412 (2009) Compound C1 was considered an effective inhibitor of ABL1(T315I), ABL1(G250E), ABL1(Y253F) and ABL1(E255K), and a partially effective inhibitor of ABL1(F317L). No other test compound in Table 5 of this Example was considered an effective inhibitor of four ABL1 variants and a partially effective inhibitor of one ABL1 variant. Compound C1 was considered a pan-ABL1 inhibitor according to the IC50 values reported in Table 5 of this Example. PK inhibition activity assessments for compounds herein, as measured by the labeled peptide cleavage assays (Z’LYTE™ assays), fluorescence displacement assay (LanthaScreen™ Eu Kinase Binding Assay) and ADP formation assay (Adapta™ Assay) described in this Example, are presented in FIG.3 to FIG.10C as an IC50 value and/or as a percent inhibition value. A value shown without units in FIG.3 to FIG.10C is an IC50 value in nanomolar (nM) units. A value shown as a percentage in FIG.3 to FIG.10C is percent inhibition value typically determined at a 100 nM concentration of test compound. The header of the first column of each of the tables shown in FIG. 3 to FIG.10C includes the term “Cmpd,” which designates a test compound assessed by an assay. FIG.3 to FIG.10C show PK inhibition by compounds determined by peptide cleavage and tracer displacement assays. FIG.3 shows inhibition of ABL family PKs. FIG.4 shows inhibition of BTK family PKs. FIG.5 shows inhibition of AURK family PKs. FIG.6 shows inhibition of JAK family PKs. FIG.7 shows inhibition of TRK family PKs. FIG.8 shows inhibition of RET family PKs. FIG.9A
shows inhibition of EPH family PKs. FIG.9B shows inhibition of TNK family, PLK family and IRAK family PKs. FIG.9C shows inhibition of SRC and DDR family PKs. FIG.9D shows inhibition of ABL2 and PTK2B PKs. FIG.10A shows inhibition of ABL and BTK family PKs. FIG.10B shows inhibition of ABL and AURK family PKs. FIG.10C shows inhibition of ABL, BTK and AURK family PKs. The key at the bottom of FIG.3 is applicable to charts in FIG.4 to FIG.10C. The top portion of the key is applicable to percent inhibition values and the bottom portion of the key is applicable to IC50 values. In FIG.3 to FIG.10C: (i) a “*” designation signifies that the corresponding value is an external value (for example, a value from a scientific publication); (ii) an additional row for a particular test compound within one table signifies a different manufacturing lot of the test compound; (iii) when two percentages are provided in one cell of a table, the first value is obtained at a concentration of 100 nM for the test compound and the second value is obtained at a concentration of 10 nM of the test compound; (iv) a “Lit + ve” designation signifies that the test compound was reported in an external source as exhibiting an inhibitory activity against the applicable target PK (for example, in a scientific publication); and (v) a % value and an IC50 value within one cell of a table for particular test compound are separated by brackets or by a comma (a bracket or comma separator serve the same function of separating the % value and the IC50 value). In FIG.3 to FIG.10C, the “Cmpd” column includes at the end multiple test compounds designated by a “COM” designation, which designates comparative compounds subject to clinical studies that are commercially available. The following “COM” designations are held in reserve: COM4, COM11, COM12, COM13, COM14, COM18, COM24, COM25, COM26 and COM27. Example 10: Preparation of C8, C9, C10 and C11 Provided in this Example are processes for preparing compounds C8, C9, C10 and C11 shown in Table A. Preparation of 2-Cl-8-(3,5-dimethoxyphenyl) quinazoline by Suzuki Coupling A 0.5 mL- 2.0 mL tapered microwave vial with triangular stir vane is charged with 3,5- dimethoxyphenylboronic acid. A solution of 2-chloro-8-bromo quinazoline in dioxane is added followed by aqueous K3PO4. Tetrakis(triphenylphosphine)palladium is added and the vial sealed, then heated in an aluminum block (105°C) for 5 hours. LCMS indicated the reaction is complete with the formation of the desired product. The reaction is diluted with excess iPrOAc. MgSO4 is added and the mixture filtered and evaporated to a brown oil (50 mg). The oil is chromatographed by flash chromatography. The major UV-active product is isolated.
Preparation of 3-((8-(3,5-dimethoxyphenyl)quinazolin-2-yl)amino)-4-methoxybenzaldehyde A 0.5-2.0 mL tapered microwave vial is charged with 3-amino-4-methoxybenzaldehyde. The vial is then charged with 2-Cl-8-(3,5-dimethoxyphenyl)quinazoline. EtOH is added, and the combined solids are agitated using a pipette before sealing. The mixture is placed in a 130°C aluminum block and vigorously stirred for 5 hours. The vial is rinsed with excess EtOH, then excess DCM, into a 250 mL round-bottomed (rb) flask. The solution is evaporated to an orange-brown oil. IPA (10 mL) is added and the mixture heated until the residue dissolved. The dark solution is allowed to cool and stir at room temperature for 12 hr. The dark brown precipitated solid is recovered by filtration. The product is used without further purification. Preparation of 8-(3,5-dimethoxyphenyl)-N-(2-methoxy-5-((methylamino)methyl)phenyl)quinazolin-2- amine (C8)
with 3-((8-(3,5-dimethoxyphenyl)quinazolin-2-yl)amino)-4- methoxybenzaldehyde. THF is added to effect dissolution. A solution of methylamine in THF is added followed by solid sodium triacetoxybotohydride. Acetic acid is added and the vial sealed, then stirred at rt for 16 hours. The reaction is diluted with excess iPrOAc and filtered. The filtrate is washed with 1N aqueous sodium hydroxide (2x washes). The organic phase is washed with aqueous 1N HCl (2x washes). The organic phase is set aside and the aqueous phase is adjusted to pH 12 using solid NaOH. The aqueous phase is extracted with iPrOAc. The aqueous phase is set aside and the organic phase dried over MgSO4, filtered and evaporated to an oil. The desired product is purified by flash chromatography, yielding the desired compound. Preparation of N-(5-(5,8,11-trioxa-2-azadodecyl)-2-methoxyphenyl)-8-(3,5- dimethoxyphenyl)quinazolin-2-amine (C9)
((8-(3,5-dimethoxyphenyl)quinazolin-2-yl)amino)-4- methoxybenzaldehyde. THF is added to effect dissolution. A solution of 2-(2-(2- methoxyethoxy)ethoxy)ethan-1-amine in THF is added followed by solid sodium triacetoxybotohydride. Acetic acid is added and the vial sealed, then stirred at rt for 16 hours. The reaction is diluted with excess iPrOAc and filtered. The filtrate is washed with 1N aqueous sodium hydroxide (2x washes). The organic phase is washed with aqueous 1N HCl (2x washes). The organic phase is set aside and the aqueous phase is adjusted to pH 12 using solid NaOH. The aqueous phase is extracted with iPrOAc. The aqueous phase is set aside and the organic phase dried over MgSO4, filtered and evaporated to an oil. The desired product is purified by flash chromatography, yielding the desired compound. Preparation of 8-(3,5-dimethoxyphenyl)-N-(5-(2-(3-((8-(3,5-dimethoxyphenyl)quinazolin-2-
-4- methoxybenzaldehyde. THF is added to effect dissolution. A solution of N-(5-(5,8,11-trioxa-2- azadodecyl)-2-methoxyphenyl)-8-(3,5-dimethoxyphenyl)quinazolin-2-amine in THF is added
followed by solid sodium triacetoxybotohydride. Acetic acid is added and the vial sealed, then stirred at rt for 16 hours. The reaction is diluted with excess iPrOAc and filtered. The filtrate is washed with 1N aqueous sodium hydroxide (2x washes). The organic phase is washed with aqueous 1N HCl (2x washes). The organic phase is set aside and the aqueous phase is adjusted to pH 12 using solid NaOH. The aqueous phase is extracted with iPrOAc. The aqueous phase is set aside and the organic phase dried over MgSO4, filtered and evaporated to an oil. The desired product is purified by flash chromatography, yielding the desired compound. Preparation of 8-(3,5-dimethoxyphenyl)-N-(5-(((3-((8-(3,5-dimethoxyphenyl)quinazolin-2-yl)amino)- 4-methoxybenzyl)(methyl)amino)methyl)-2-methoxyphenyl)quinazolin-2-amine (C11)
quinazolin-2-yl)amino)-4- methoxybenzaldehyde. THF is added to effect dissolution. A solution of 8-(3,5-dimethoxyphenyl)-N- (2-methoxy-5-((methylamino)methyl)phenyl)quinazolin-2-amine in THF is added followed by solid sodium triacetoxybotohydride. Acetic acid is added and the vial sealed, then stirred at rt for 16 hours. The reaction is diluted with excess iPrOAc and filtered. The filtrate is washed with 1N aqueous sodium hydroxide (2x washes). The organic phase is washed with aqueous 1N HCl (2x washes). The organic phase is set aside and the aqueous phase is adjusted to pH 12 using solid NaOH. The aqueous phase is extracted with iPrOAc. The aqueous phase is set aside and the organic phase dried over MgSO4, filtered and evaporated to an oil. The desired product is purified by flash chromatography, yielding the desired compound. Example 11: 9H-fluoren-9-ylmethyl N-[5-(tert-butoxycarbonylamino)-2-methyl- phenyl]carbamate (Compound A) Examples 11-14 are for preparing C12. In this Example 11, provided is a process for preparing a compound having the following structure: H H N N .
A 250 mL round bottom flask with stir bar was charged with DCM (50 mL). Solid tert-butyl N-(3- amino-4-methyl-phenyl)carbamate (1.98 g, 8.908 mmol) was added and the mixture stirred until dissolution was complete. DIEA (1.86 mL, 10.689 mmol) was added, followed by Fmoc-Cl (2.765 g, 10.689 mmol). The reaction was stirred at room temperature overnight. The suspension of white solid was filtered and the filtrate evaporated to a white solid. The white solid was suspended in EtOAc (50 mL) and filtered again. The filtrate was evaporated to the title compound (white solid, 3.804 g). The product was taken forward into the next step without further purification. Example 12: 9H-fluoren-9-ylmethyl N-(5-amino-2-methyl-phenyl)carbamate hydrochloride (Compound B) The compound having the following structure was prepared: .
(rb) flask containing 9H-fluoren-9-ylmethyl N-[5-(tert- butoxycarbonylamino)-2-methyl-phenyl]carbamate was charged with DCM (50 mL). TFA (10 mL) was added and the yellow suspension became homogenous and turned dark brown in 1 hour (hr). The solution was stirred at room temperature overnight. Toluene (20 mL) was added, and the reaction evaporated to a dark residue (9.205 g). The residue was dissolved in iPrOAc (100 mL) in a 250 mL rb flask with stirrer.1N HCl (50 mL) was added and the mixture vigorously stirred for 2 hr. A voluminous white solid precipitated. The solid was recovered by filtration from the two-phase mother liquor. The solid in the filter funnel was allowed to stand under lyophilizer vacuum overnight. LCMS showed it is the title compound as the HCl salt (1.132 g). Example 13: 9H-fluoren-9-ylmethyl N-[5-[(8-bromoquinazolin-2-yl)amino]-2-methyl- phenyl]carbamate (Compound C) The compound having the following structure was prepared: .
– with stir bars were each charged with [3-(9H-fluoren-9- ylmethoxycarbonylamino)-4-methyl-phenyl]ammonium;chloride (526 mg, 1.381 mmol). Dioxane (10
mL) was added to each vial and the mixture stirred for 5 min to effect complete suspension. While stirring, each vial was then charged with 8-bromo-2-chloro-quinazoline (673 mg, 2.762 mmol). The vials were sealed and heated in an aluminum block (125°) for 1.5 hr. Each reaction becomes a dark orange homogenous solution. The vials were capped with a rubber septum and vigorously stirred at room temperature for 2 hr. The bright orange precipitate was recovered by filtration (filtration was slow), then allowed to stand under lyophilizer vacuum for 3 days, affording the title compound (1.232 g). Example 14: 4-((2-methyl-5-((8-phenylquinazolin-2-yl)amino)phenyl)carbamoyl)benzoic acid The title compound having the following structure was prepared (C12): .
Compound C, 3-(4- (ethoxycarbonyl)benzamido)benzenaminium 2,2,2-trifluoroacetate was converted to ethyl 4-((5-((8- bromoquinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoate. A 10-20 mL microwave vial was charged with 9H-fluoren-9-ylmethyl N-[5-[(8-bromoquinazolin-2- yl)amino]-2-methyl-phenyl]carbamate (938 mg, 1.701 mmol). Dioxane (12 mL) was added and the mixture stirred for 1 hr at room temperature to effect complete suspension. ethyl 4-((5-((8- bromoquinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoate (505 mg, 2.552 mmol) was added followed by aqueous (aq) K3PO4 (2M, 2.6 mL, 5.103 mmol). Solid K3PO4 was added (361 mg, 1.701 mmol). Tetrakistriphenylphosphine palladium (393 mg, 0.340 mmol) was added. The vial was sealed and heated in an aluminum block (110 degrees C) for 16 hr. The mixture, containing a yellow solid suspended in the two-phase dioxane/water solvent, was poured into iPrOAc (~100 mL). The solid dissolved. The mixture was transferred to a separatory funnel and the lower aqueous was removed and set aside. The clear, brown organic was dried over MgSO4 and filtered into a 250 mL rb flask. The filtrate was evaporated down to about 50 mL volume, then treated with 1N HCl (50 mL). The orange mixture was vigorously stirred overnight. The two-phase mixture consisted of a deep yellow aqueous phase and a brown organic phase with a small amount of insoluble residue floating at the interface. The mixture was transferred to a separatory funnel. The slightly turbid aqueous was slowly drawn off to avoid taking any of the insoluble material. The remaining organic was returned to the rb flask and combined with 1N HCl (50 mL). The mixture was vigorously stirred for 1 hr, then carefully partitioned again. The combined
aqueous phase was placed into another rb flask and combined with iPrOAc (75 mL), then vigorously stirred for 1 hr. The now clear yellow aqueous was recovered. The aqueous phase was evaporated on a rotary evaporator (rotovap) and the resultant yellow solid was allowed to stand under lyophilizer vacuum overnight, affording ethyl 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoate as a yellow/orange solid (490 mg). A 10 - 20 mL microwave vial was charged with ethyl 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoate. Tetrahydrofuran (THF) was added and the mixture stirred for 1 min to effect full suspension. LiOH hydrate (10 equivalents) was added, followed by water (10 equivalents). The vial was sealed and heated in an aluminum block (85°) for 24 hr. The solid/liquid mixture was treated with THF and excess 1N HCl. The solid dissolved. The mixture was transferred, using EtOAc, in portions, into a screw top vial and evaporated free of organics, leaving a clear aqueous and a suspended solid. The aqueous phase was removed by a syringe. The solid was rinsed twice more with hot water. Each time the water was allowed to cool and was removed by a syringe. The solid was allowed to stand under lyophilizer vacuum overnight, affording the title compound. Example 15: Preparation of C13 A nucleophilic aromatic substitution (SNAr) was performed:
with ethyl 4-((3-amino- 4-methylphenyl)carbamoyl)benzoate (189 mg, 0.63 mmol). EtOH (3.17 mL) was added and the mixture stirred until significant dissolution was obtained.8-bromo-2-chloro-quinazoline (309 mg, 1.27 mmol) was added. The vial was sealed and heated, with stirring, in an aluminum block (120°C) for 5 hours. The reaction was poured into excess iPrOAc and washed with sat aq sodium bicarbonate (3x). The organic layer was dried over MgSO4, filtered and concentrated under reduced pressure. The derived residue was purified by pTLC (40:1 DCM:MeOH). The band corresponding to product was isolated (rf: 0.4) and used for the next reaction, which was a brown solid (18.7 mg, 6% yield). A Suzuki coupling process then was performed:
(3-((8- bromoquinazolin-2-yl)amino)-4-methylphenyl)carbamoyl)benzoate (18.7 mg, 0.037 mmol, 1 equiv), (phenyl)boronic acid (6.8 mg, 0.056 mmol, 1.5 equiv), K3PO4 (24 μL, 2M, 0.11 mmol, 3 equiv), and dioxane (0.2 mL, 0.18 M). Tetrakis(triphenylphosphine)palladium (8.55 mg, 0.007 mmol) was added, and the vial sealed, then heated in an aluminum block (105°C) for 5 hours. The reaction was diluted with excess iPrOAc and dried over MgSO4. Filtration and evaporation afforded a yellow solid. The crude material was purified by pTLC (40:1 CH2Cl2:MeOH). One band was isolated containing pure product (5.7 mg, 39% yield). An ester hydrolysis then was performed: a suspension of
ethyl 4-((3-((8-bromoquinazolin-2-yl)amino)-4-methylphenyl)carbamoyl)benzoate (11 mg, 0.022 mmol) in THF (0.39 mL). Water (110 uL, 0.221 mmol) was added followed by LiOH hydrate (9.3 mg, 0.221 mmol). The vial was sealed and heated in an aluminum block (85°C) for 24 hr. Most of the material dissolved leaving a yellow organic phase and a clear aqueous phase and was then evaporated. The solid was then treated with THF (0.2 mL) and 0.1N HCl 1x and with water 3x. The organic phase was evaporated off and the aqueous phase was drawn off. The dark suspension of solid was allowed to stand under lyophilizer vacuum for two hours. Pure product was obtained (7.1 mg, 68% yield). Example 16: Preparation of C14 An Fmoc protection was performed:
with tert-butyl (3-amino-4- ethylphenyl)carbamate (1.072 g, 4.82 mmol). DCM (20 mL) was added and the mixture stirred until dissolution was complete. DIEA (1.01 mL, 5.79 mmol) was added, followed by solid Fmoc-Cl (1.50
g, 5.79 mmol). The pale yellow solution was stirred at room temperature. After 4 hr the reaction had turned into a solid mass of white precipitate. DCM (5 mL) was added to aid in suspension and stirring. A sample of the suspension for LCMS was removed and partitioned between iPrOAc and aqueous bicarb phases. The organic phase was evaporated to a white solid. The solid was layered with acetone, yielding a turbid solution which was injected into a LCMS, showing the reaction was complete. The reaction, which was still a white suspension, was poured into a vigorously stirred mixture of saturated bicarb and iPrOAc. The white suspension did not dissolve after stirring for 15 min. The mixture was transferred to a 500 mL separation funnel with liberal iPrOAc rinsing. The slightly turbid, colorless aqueous phase was removed and the organic white suspension was washed twice more with bicarbonate and then water. The aqueous layers were removed each time without any significant emulsification. The organic phase was allowed to stand overnight in the separation funnel. There was a layer of white suspended material beneath a clear supernatant. The white flocculent material was mostly recovered and temporarily set aside. The iPrOAc organic phase was dried over MgSO4, filtered and evaporated to a white solid. The suspended material was stirred with excess DCM. Everything dissolved, leaving behind the DCM lower layer along with a small amount of water. The DCM layer was recovered, dried over MgSO4, filtered and evaporated to a white solid. The solid was allowed to stand under high vacuum overnight. The two materials were qualitatively identical by LCMS. Total weight = 2.356 g (110% yield; theoretical yield was 2.142 g). The materials were combined for the next process. A Boc removal process then was performed: A 250 mL round of (9H-fluoren-9-
yl)methyl tert- g, batch # EXP-23- KU5930) in DCM (75 mL). TFA (15 mL) was added dropwise at room temperature by pipet. The initially pale yellow suspension of white solid became a turbid orange solution. The reaction was stirred at room temperature for 2 hr. LCMS showed the reaction was complete. Toluene (30 mL) was added and the reaction evaporated to a residue. The residue was partitioned between excess iPrOAc and aqueous bicarbonate. The organic phase was dried over MgSO4, filtered and evaporated to a pale yellow solid (2.165 g). An amidation process then was performed:
methyl N-(5-amino- 2-methylphenyl) carbamate (248 mg, 0.720 mmol). DMF (4 mL) was added and the mixture stirred until dissolution was complete.4-ethoxycarbonylbenzoic acid (252 mg, 1.296 mmol) was added and the mixture stirred until homogenous. TEA (181 μL, 1.296 mmol) was added followed by EEDQ (321 mg, 1.296 mmol). The homogenous reaction was stirred at room temperature for 24 hr. LCMS shows the reaction was nearly, but not complete done. Another charge of EEDQ (150 mg, 0.607 mmol) was added and the solution stirred at room temperature for another 7 hr. LCMS showed little change. TEA (180 μL, 1.296 mmol) was added and the solution stirred at room temperature overnight. LCMS showed somewhat less recovered starting material. The peak at 5.15 no longer showed the 521.206 mass peak. The peak at 4.12 corresponded to the theoretical mass and isotopic distribution of the aniline product resulting from loss of Fmoc from the initial amidation reaction. The reaction was partitioned between excess iPrOAc and saturated bicarbonate. The organic phase was washed with bicarbonate (2x more), then water (no acid wash). The organic phase was dried over MgSO4, filtered and evaporated to a dark oil (726 mg). The oil was dissolved in iPrOAc and washed with 1N HCl (3x wash). The aqueous phase was sampled for LCMS and showed the deprotected product in usable condition. The aqueous phase was layered with excess iPrOAc and basified with solid NaHCO3. The organic phase was recovered, dried over MgSO4, filtered and evaporated to a dark residue (304 mg), which was used in the next step. A nucleophilic aromatic substitution (SNAr) then was performed:
- charged with ethyl 4-[(3-amino-4-methyl-phenyl)carbamoyl]benzoate (304 mg total, 1.019 mmol). EtOH (6.0 mL total) was added followed by 8-bromo-2-chloro-quinazoline (1.241 g, 5.095 mmol). The mixtures were heated in an aluminum block (125°C) for a total of 4 hours. LCMS shows the reaction is complete and the desired product is present in all three vials. The reaction mixtures from the three vials were combined and evaporated to a yellow solid. The solid was digested in IPA at reflux, then stirred overnight at room temperature. The light brown solid was recovered by filtration (1.010 g).
The solid was suspended in DCM (5 mL). Not all of it dissolved. The clear orange/brown supernatant was loaded onto a 24g normal phase column and eluted with a DCM/MeOH gradient (0% to 10% MeOH in DCM, 7 column volumes, then 10% MeOH in DCM 6 column volumes). The more retained peak was collected (54 mg obtained). A Suzuki coupling process then was performed:
bromoquinazolin-2-yl)amino]-4-methyl-benzoyl]amino]benzoate (54 mg, 0.017 mmol). Dioxane (1 mL) was added followed by (4-fluoro-2-isopropoxy-phenyl)boronic acid (32 mg, 0.160 mmol). The mixture was stirred to effect suspension, then aqueous K3PO4 (2M, 160 μL, 0.321 mmol) was added. The vial was sealed and heated in an aluminum block (105°C) for 4 hours. The dark but clear solution was sampled for LCMS and the desired product was detected. The reaction was diluted with excess iPrOAc and dried over MgSO4. The mixture was filtered and evaporated to an orange/brown oil (116 mg). The oil was chromatographed on three 500 μM pTLC plates using 40:1 DCM/MeOH. The major band was collected and evaporated to a light yellow oil (47 mg). An ester hydrolysis then was performed:
of ethyl 4-[[3-[[8-(4-fluoro-2-isopropoxy-phenyl)quinazolin-2-yl]amino]-4-methyl-phenyl]carbamoyl]benzoate (47 mg, 0.081 mmol) in THF (1.5 mL). LiOH hydrate (34 mg, 0.812 mmol) was added followed by water (20 μL, 1.110 mmol). The vial was sealed and heated for 8 hours in an aluminum block (85°C) while stirring. The yellow mixture was treated with 1N HCl (2 mL). The suspended solid initially dissolved but with further stirring a new solid precipitated. The mixture was transferred to a 40 mL screw top vial and the organics evaporated. The water and solid mixture was diluted with more water (2 mL) and brought to a boil, then allowed to cool with the vial clamped at an angle such that the solid could settle to the bottom of the mixture and leave the supernatant above. The slightly turbid supernatant was drawn off by a syringe. The procedure was repeated two more times. The wet solid was lyophilized overnight resulting in a light yellow solid (37 mg).
* * * The entirety of each patent, patent application, publication and document referenced herein is incorporated by reference. Citation of patents, patent applications, publications and documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents. Their citation is not an indication of a search for relevant disclosures. All statements regarding the date(s) or contents of the documents is based on available information and is not an admission as to their accuracy or correctness. The technology has been described with reference to specific implementations. The terms and expressions that have been utilized herein to describe the technology are descriptive and not necessarily limiting. Certain modifications made to the disclosed implementations can be considered within the scope of the technology. Certain aspects of the disclosed implementations suitably may be practiced in the presence or absence of certain elements not specifically disclosed herein. Each of the terms “comprising,” “consisting essentially of,” and “consisting of” may be replaced with either of the other two terms. The term “a” or “an” can refer to one of or a plurality of the elements it modifies (e.g., “a reagent” can mean one or more reagents) unless it is contextually clear either one of the elements or more than one of the elements is described. The term “about” as used herein refers to a value within 10% of the underlying parameter (i.e., plus or minus 10%; e.g., a weight of “about 100 grams” can include a weight between 90 grams and 110 grams). Use of the term “about” at the beginning of a listing of values modifies each of the values (e.g., “about 1, 2 and 3” refers to "about 1, about 2 and about 3"). When a listing of values is described, the listing includes all intermediate values and all fractional values thereof (e.g., the listing of values "80%, 85% or 90%" includes the intermediate value 86% and the fractional value 86.4%). When a listing of values is followed by the term "or more," the term "or more" applies to each of the values listed (e.g., the listing of "80%, 90%, 95%, or more" or "80%, 90%, 95% or more" or "80%, 90%, or 95% or more" refers to "80% or more, 90% or more, or 95% or more"). When a listing of values is described, the listing includes all ranges between any two of the values listed (e.g., the listing of "80%, 90% or 95%" includes ranges of "80% to 90%," "80% to 95%" and "90% to 95%"). Certain implementations of the technology are set forth in the claim(s) that follow(s).
Claims
What is claimed is: 1. A compound of Formula A: A
R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R4, R5 and R6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo.
2. The compound of claim 1, wherein R1, R2 and R3 each independently is hydrogen, methyl or methoxy.
3. The compound of claim 1 or 2, wherein R4, R5 and R6 each independently is hydrogen, F, isopropyl, or isopropyloxy.
4. The compound of any one of claims 1-3, wherein one of R1, R2 and R3 is methyl or methoxy and two of R1, R2 and R3 are hydrogen.
5. The compound of any one of claims 1-4, wherein R1, R2 and R3 each is hydrogen.
6. The compound of any one of claims 1-5, wherein R5 is hydrogen.
7. The compound of any one of claims 1-6, wherein R4, R5 and R6 each is hydrogen.
8. The compound of any one of claims 1-7, wherein R1 is methyl or methoxy and R2 and R3 each is hydrogen.
9. The compound of any one of claims 1-8, wherein R1 is methyl and R2 and R3 each is hydrogen.
10. The compound of any one of claims 1-7, wherein R3 is methyl or methoxy and R1 and R2 each is hydrogen.
11. The compound of any one of claims 1-7 and 10, wherein R3 is methyl and R1 and R2 each is hydrogen.
12. The compound of claim 1, wherein R1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; R2, R3 and R5 each is hydrogen; and R4 and R6 each independently is hydrogen, optionally substituted C1-C4 alkyl, optionally substituted C1-C4 alkoxy, or halo, with the proviso that R4 or R6 , or R4 and R6, is not hydrogen.
13. The compound of claim 12, wherein R1 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
14. The compound of claim 12 or 13, wherein (i) R4 is unsubstituted C1-C4 alkoxy or isopropyloxy; (ii) R6 is fluoro or chloro; or a combination of (i) and (ii).
15. The compound of any one of claims 12-14, which is 4-((5-((8-(4-fluoro-2- isopropoxyphenyl)quinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C1); 4-((5-((8-(4-fluoro-2-isopropoxyphenyl)quinazolin-2-yl)amino)-2- methoxyphenyl)carbamoyl)benzoic acid (compound C3); 4-((5-((8-(2- isopropylphenyl)quinazolin-2-yl)amino)-2-methylphenyl)carbamoyl)benzoic acid (compound C4); or a pharmaceutically acceptable salt thereof.
16. The compound of claim 1, wherein R1 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R2, R3, R4, R5 and R6 each is hydrogen.
17. The compound of claim 16, wherein R1 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
18. The compound of claim 16 or 17, which is 4-((2-methyl-5-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid or a pharmaceutically acceptable salt thereof.
19. The compound of claim 1, wherein R3 is an optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R1, R2, R4, R5 and R6 each is hydrogen.
20. The compound of claim 19, wherein R3 is an unsubstituted C1-C4 alkyl, ethyl or methyl.
21. The compound of claim 19 or 20, which is 4-((4-methyl-3-((8-phenylquinazolin-2- yl)amino)phenyl)carbamoyl)benzoic acid (compound C13) or a pharmaceutically acceptable salt thereof.
22. A compound of Formula B: R2 Formula B
or a pharmaceutically acceptable salt thereof, wherein:
R1, R2 and R3 each independently is hydrogen, optionally substituted C1-C4 alkyl or optionally substituted C1-C4 alkoxy; and R7, R8 and R9 each independently is hydrogen or optionally substituted C1-C6 alkyl.
23. A pharmaceutical composition comprising a compound of any one of claims 1-22 and a pharmaceutically acceptable excipient.
24. Use of a compound or composition of any one of claims 1-23, for inhibiting a protein kinase.
25. The use of claim 24, wherein the protein kinase is a RET family protein kinase, a TYK family protein kinase and/or a PLK family protein kinase.
26. Use of a compound or composition of any one of claims 1-23, for treatment of a medical condition or for preparation of a medicament for treatment of a medical condition.
27. The use of claim 26, wherein the medical condition is a cancer.
28. The use of claim 27, wherein the cancer is a lung cancer, a thyroid cancer, a colon cancer or a skin cancer.
29. The use of claim 28, wherein: the lung cancer is a lung nodule cancer, non-small cell lung cancer (NSCLC), small cell lung cancer, lung adenocarcinoma or mesothelioma; the thyroid cancer is medullary thyroid cancer (MTC), papillary thyroid cancer (PTC) or thyroid gland medullary carcinoma; the colon cancer is colon adenocarcinoma; and/or the skin cancer is melanoma or cutaneous melanoma.
30. The use of claim 28 or 29, wherein the cancer is associated with a RET family PK aberration.
31. The use of any one of claims 28-30, wherein the compound effectively inhibits or moderately inhibits a RET family PK.
32. The use of any one of claims 28-31, wherein the compound is of any one of claims 1-21 or optionally is of any one of claims 16-18.
33. The use of claim 27, wherein the cancer is a liver cancer, breast cancer or acute myelogenous leukemia (AML).
34. The use of claim 33, wherein the cancer is associated with a PLK family PK aberration and optionally of a PLK4 family PK aberration.
35. The use of claim 33 or 34, wherein the compound effectively inhibits or moderately inhibits a PLK family PK.
36. The use of any one of claims 33-35, wherein the compound is of any one of claims 1-21 or optionally any one of claims 19-21.
37. The use of claim 26, wherein the medical condition is a psoriasis, optionally a moderate to severe psoriasis, optionally a moderate to severe plaque psoriasis, and/or optionally is treated in a subject who is a candidate for systemic therapy or phototherapy.
38. The use of claim 37, wherein the medical condition is associated with a TYK family PK aberration and optionally is associated with a TYK2 PK aberration.
39. The use of claim 37 or 38, wherein the compound effectively inhibits or moderately inhibits TYK2.
40. The use of any one of claims 37-39, wherein the compound is of any one of claims 1-21 or optionally is of any one of claims 16-18.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202363488429P | 2023-03-03 | 2023-03-03 | |
| US202463554855P | 2024-02-16 | 2024-02-16 | |
| PCT/US2024/017890 WO2024186580A1 (en) | 2023-03-03 | 2024-02-29 | Protein kinase inhibitors and uses thereof |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| EP4676601A1 true EP4676601A1 (en) | 2026-01-14 |
Family
ID=90468893
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| EP24714122.9A Pending EP4676601A1 (en) | 2023-03-03 | 2024-02-29 | Protein kinase inhibitors and uses thereof |
Country Status (2)
| Country | Link |
|---|---|
| EP (1) | EP4676601A1 (en) |
| WO (1) | WO2024186580A1 (en) |
Family Cites Families (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US4938949A (en) | 1988-09-12 | 1990-07-03 | University Of New York | Treatment of damaged bone marrow and dosage units therefor |
| US5624677A (en) | 1995-06-13 | 1997-04-29 | Pentech Pharmaceuticals, Inc. | Controlled release of drugs delivered by sublingual or buccal administration |
| EP3270694A4 (en) * | 2015-02-17 | 2018-09-05 | Neupharma, Inc. | Certain chemical entities, compositions, and methods |
-
2024
- 2024-02-29 EP EP24714122.9A patent/EP4676601A1/en active Pending
- 2024-02-29 WO PCT/US2024/017890 patent/WO2024186580A1/en not_active Ceased
Also Published As
| Publication number | Publication date |
|---|---|
| WO2024186580A1 (en) | 2024-09-12 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN116528868B (en) | Tricyclic KRAS G12C inhibitors | |
| EP3867251B1 (en) | Kras g12c inhibitors | |
| JP6093890B2 (en) | Phenothiazinediaminium salts and their use | |
| JP6275846B2 (en) | Heteroarylpyridone and aza-pyridone compounds having electrophilic functional groups | |
| ES2732026T3 (en) | Acid addition salt of a Trk inhibitor compound | |
| CN105611923B (en) | Sodium Channel Modulators for Pain and Diabetes | |
| WO2019079701A1 (en) | Heterobifunctional compounds with improved specificityfor the bromodomain of brd4 | |
| JP7810640B2 (en) | Therapeutic Conjugates | |
| KR102605546B1 (en) | Pyrimidopyrimidinones useful as Wee-1 kinase inhibitors | |
| EA024984B1 (en) | 6-CYCLOALKYL-1,5-DIHYDRO-PYRAZOLO[3,4-d]PYRIMIDIN-4-ONE DERIVATIVES AND THEIR USE AS PDE9A INHIBITORS | |
| WO2008118626A2 (en) | Inhibitors of jnk and methods for identifying inhibitors of jnk | |
| CN105611930A (en) | Spiro-quinoxaline derivatives as inhibitors of non-apoptotic regulated cell-death | |
| CN107531683A (en) | USP7 inhibitor compounds and methods of use | |
| EP4374157A2 (en) | Fret-based assays | |
| WO2025218831A2 (en) | Thiadiazolidinone derivative with ptpn2/ptpn1 inhibitory activity, and preparation method therefor and use thereof | |
| WO2024186580A1 (en) | Protein kinase inhibitors and uses thereof | |
| WO2023220722A2 (en) | Pak1 degraders and methods of use thereof | |
| WO2026050773A1 (en) | Protein kinase inhibitors and uses thereof | |
| EP4676600A1 (en) | Protein kinase inhibitors and uses thereof | |
| JP6970667B2 (en) | Quinoline amide and its usage | |
| CN115244054B (en) | Crystals of hypoxanthine compound | |
| CN110229146B (en) | Histone deacetylase inhibitor and preparation method and application thereof | |
| Kim et al. | Development of reversible covalent PPARγ antagonistic ligands based on a structure-based approach | |
| WO2026082160A1 (en) | Wee1 protein degradation agent and use thereof | |
| CN114426541A (en) | Azaaryl compounds and uses thereof |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| STAA | Information on the status of an ep patent application or granted ep patent |
Free format text: STATUS: UNKNOWN |
|
| STAA | Information on the status of an ep patent application or granted ep patent |
Free format text: STATUS: THE INTERNATIONAL PUBLICATION HAS BEEN MADE |
|
| PUAI | Public reference made under article 153(3) epc to a published international application that has entered the european phase |
Free format text: ORIGINAL CODE: 0009012 |
|
| STAA | Information on the status of an ep patent application or granted ep patent |
Free format text: STATUS: REQUEST FOR EXAMINATION WAS MADE |
|
| 17P | Request for examination filed |
Effective date: 20251001 |
|
| AK | Designated contracting states |
Kind code of ref document: A1 Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC ME MK MT NL NO PL PT RO RS SE SI SK SM TR |