Patent Grant
9157077
Casein kinase 1 (CK1) is a family of evolutionarily conserved serine/threonine kinases including seven known members in vertebrates (CK1α, -β, -γ1, -γ2, -γ3, -δ and -ε). The CK1s contain a typical kinase domain followed by a C-terminal tail region, which has been implicated in the regulation of CK1 localization, substrate selectivity and kinase activity. Myriad proteins have been found to be phosphorylated by CK1s, which are involved in a wide range of cellular functions including vesicular trafficking, DNA damage repair, cell cycle progression, cytokinesis and circadian rhythms (reviewed by Gross and Anderson (1998); Vielhaber and Virshup (2001); Knippschild et al. (2005)). Moreover, CK1 family members (-α, -δ/ε and -γ) modulate the activities of major signaling pathways (for example, Wnt and Shh) through several mechanisms (Peters et al., 1999; Liu et al., 2002; Price and Kalderon, 2002; Davidson et al., 2005; Zeng et al., 2005 and reviewed by Price (2006)).
In mammals seven CK1 isoforms, namely CK1α, γ, γ1-3, δ and ε, and several splice variants have been described. They all contain a highly conserved kinase domain, a short N-terminal domain of 6 to 76 amino acids and a highly variable C-terminal domain of 24 to more than 200 amino acids. The constitutive phosphotransferase activity of CK1 isoforms is tightly controlled by several mechanisms. For example, the closely related isoforms CK1δ and ε, which share a 98% identity at the amino acid level in their catalytic domain, are regulated by autophosphorylation, dephosphorylation and proteolytic cleavage. Members of the CK1 family are found in the nucleus, the cytoplasm and in the plasma membrane. By phosphorylating many different substrates bearing either a canonical or non-canonical consensus sequence they modulate the activity of key regulator proteins involved in many cellular processes such as cell differentiation, cell proliferation, apoptosis, circadian rhythm, chromosome segregation, and vesicle transport.
The Pim kinase family contains three isoforms, Pim-1, Pim-2 and Pim-3, and has recently emerged as targets of interest in oncology and immune regulation. Ongoing studies have identified a role for these proteins in cell survival and proliferation, both functionally and mechanistically, and overexpression has been observed in a number of human cancers and inflammatory states.
Pim kinases suppress apoptosis and regulate cell-cycle progression. Elevated levels of Pim kinases have been reported in solid tumors such as prostate cancer and pancreatic cancer. Pim-1 was initially discovered in murine leukemia and several independent studies have shown this kinase to be upregulated in human prostate cancer. Pim-1, 2 and 3 make up a distinct and highly homologous family of serine/threonine kinases belonging to the calmodulin-dependent protein kinase-related (CAMK) family. In addition to the three gene-encoded proteins, translational variants have also been reported for Pim-1 and 2 resulting from utilization of alternative start codons. The name Pim refers to the original identification of the pim-1 gene as a frequent proviral insertion site in Moloney murine leukemia virus-induced T-cell lymphomas, and the gene encoding Pim-2 was subsequently found to have similar susceptibility. Pim-3, originally designated kinase induced by depolarization (KID)-1, was later renamed due to high sequence similarity to Pim-1 (71% identity at the amino acid level). Considering all three isoforms, Pim proteins are widely expressed with high levels in hematopoietic tissue and are aberrantly expressed in a variety of human malignancies. Pim kinases positively regulate cell survival and proliferation, affording therapeutic opportunities in oncology. The Pim protein kinases are frequently overexpressed in prostate cancer and certain forms of leukemia and lymphoma.
A role for Pim kinases in immune regulation has also been observed. Pim-2 has been reported to have enhanced levels of expression in a variety of inflammatory states and may function as a positive regulator of interleukin-6 (IL-6), whereby overexpression of the kinase augments stimulus-induced IL-6 levels. Pim-1 and 2 have also been implicated in cytokine-induced T-cell growth and survival. Comparing the sensitivity of stimulated T cells from Pim-1−/−Pim-2−/− mice to wild-type mice following treatment with the immunosuppressant rapamycin, it was found that T-cell activation was significantly impaired by Pim-1/Pim-2 deficiency, suggesting that Pim kinases promote lymphocyte growth and survival through a PI3K/AKT (PKB, protein kinase B)/mammalian target of rapamycin (mTOR)-independent pathway. Other parallel but independent functions and overlapping substrate specificity for proteins in these pathways have been reported as well, including the positive regulation of transcription of nuclear factor kappa-B (NF-κB)-responsive genes, which have implications in both inflammation and oncology. Therefore, Pim kinases are attractive targets for both therapeutic areas. Further, Pim kinases have been reported to play a role in the protection of the ATP-binding cassette (ABC) transporter P-glycoprotein (Pgp; ABCB1) from proteolytic and proteasomal degradation. Pgp is known to mediate drug efflux and as such, inhibitors of Pim kinases may provide a novel approach to abrogating drug resistance.
An aspect of the present invention relates to compounds that inhibit casein kinase 1 and/or casein kinase 2 and/or a PIM kinase. For example, an embodiment relates to a compound of formula 1:
or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
wherein any one of the aforementioned alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl, and heterocyclylalkyl may be optionally substituted.
An embodiment relates to a compound of formula 2:
or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
wherein any one of the aforementioned alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl, and heterocyclylalkyl may be optionally substituted.
An aspect of the invention relates to a compound, or a pharmaceutically acceptable salt thereof, selected from the group consisting of:
An aspect of the invention relates to a compound, or a pharmaceutically acceptable salt thereof, selected from the group consisting of:
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of CK1, CK1γ1, CK1γ2, or CK1γ3. In one embodiment the compound has an IC50 of less than 5000 nM for CK1, CK1γ1, CK1γ2, or CK1γ3. In one embodiment the compound has an IC50 of less than 1000 nM for CK1, CK1γ1, CK1γ2, or CK1γ3. In one embodiment the compound has an IC50 of less than 500 nM for CK1, CK1γ1, CK1γ2, or CK1γ3.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of CK2. In one embodiment the compound has an IC50 of less than 5000 nM for CK2. In one embodiment the compound has an IC50 of less than 1000 nM for CK2. In one embodiment the compound has an IC50 of less than 500 nM for CK2.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of PIM1, PIM2, or PIM3. In one embodiment the compound has an IC50 of less than 5000 nM for PIM1, PIM2, or PIM3. In one embodiment the compound has an IC50 of less than 1000 nM for PIM1, PIM2, or PIM3. In one embodiment the compound has an IC50 of less than 500 nM for PIM1, PIM2, or PIM3.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of the Wnt pathway.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of the TGFβ pathway.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of the JAK/STAT pathway.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is an inhibitor of the mTOR pathway.
An embodiment relates to any one of the aforementioned compounds, wherein the compound is a modulator of Pgp degradation, drug efflux, or drug resistance.
An embodiment relates to a pharmaceutical composition comprising any one or combination of the aforementioned compounds, and a pharmaceutically acceptable carrier.
Another embodiment relates to a method of inhibiting CK1 activity, comprising contacting CK1, CK1γ1, CK1γ2, or CK1γ3 with any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of inhibiting CK2 activity, comprising contacting CK2 with any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating or preventing a condition associated with aberrant CK1, CK1γ1, CK1γ2, or CK1γ3 activity, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating or preventing a condition associated with aberrant CK2 activity, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating cancer, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions. In one embodiment the cancer is a cancer of a system selected from the group consisting of the hematopoietic system, immune system, endocrine system, pulmonary system, gastrointestinal system, musculoskeletal system, reproductive system, central nervous system, and urologic system. In one embodiment the cancer is located in the mammal's myeloid tissues, lymphoid tissues, pancreatic tissues, thyroid tissues, lung tissues, colon tissues, rectal tissues, anal tissues, liver tissues, skin, bone, ovarian tissues, uterine tissues, cervical tissues, breast, prostate, testicular tissues, brain, brainstem, meningeal tissues, kidney or bladder. In one embodiment the cancer is selected from the group consisting of breast cancer, colon cancer, multiple myeloma, prostate cancer, Hodgkin's lymphoma, non-Hodgkin's lymphoma, leukemia, hematologic malignancy, renal cell carcinoma, renal cancer, malignant melanoma, pancreatic cancer, lung cancer, colorectal carcinoma, brain cancer, head and neck cancer, bladder cancer, thyroid cancer, ovarian cancer, cervical cancer, and myelodysplastic syndrome.
Another embodiment relates to a method of treating leukemia or other hematologic malignancies, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating Alzheimer's disease, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating a Wnt-dependent disease, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating a TGFβ-dependent disease, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating a JAK/STAT-dependent disease, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating an mTOR-dependent disease, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating or preventing inflammation, inflammatory diseases (e.g., osteoarthritis and rheumatoid arthritis), neurological conditions (e.g., Alzheimer's disease) and neurodegeneration, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating or preventing bone-related diseases and conditions, including osteoporosis and bone formation, or facilitating bone restoration, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating or preventing hypoglycemia, metabolic syndrome and diabetes, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of influencing apoptosis (e.g., increasing the rate of apoptosis in cancerous cells), comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of treating or preventing aberrant embryonic development, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of inhibiting PIM activity, comprising contacting PIM1, PIM2 or PIM3 with any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method for treating or preventing a condition associated with aberrant PIM activity, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method of modulating Pgp degradation and/or drug efflux activity, comprising contacting a cell with any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method for treating a malignancy based upon modulation of Pgp, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions.
Another embodiment relates to a method for treating a malignancy based upon modulation of Pgp, comprising administering to a mammal in need thereof a therapeutically effective amount of any one of the aforementioned compounds or pharmaceutical compositions, in conjunction with another drug, compound, or material, to abrogate resistance to the drug, compound, or material.
Definitions
The definitions of terms used herein are meant to incorporate the present state-of-the-art definitions recognized for each term in the chemical and pharmaceutical fields. Where appropriate, illustration is provided. The definitions apply to the terms as they are used throughout this specification, unless otherwise limited in specific instances, either individually or as part of a larger group.
Where stereochemistry is not specifically indicated, all stereoisomers of the inventive compounds are included within the scope of the invention, as pure compounds as well as mixtures thereof. Unless otherwise indicated, individual enantiomers, diastereomers, geometrical isomers, and combinations and mixtures thereof are all encompassed by the present invention. Polymorphic crystalline forms and solvates are also encompassed within the scope of this invention.
As used herein, the term “isolated” in connection with a compound of the present invention means the compound is not in a cell or organism and the compound is separated from some or all of the components that typically accompany it in nature.
As used herein, the term “pure” in connection with an isolated sample of a compound of the present invention means the isolated sample contains at least 60% by weight of the compound. Preferably, the isolated sample contains at least 70% by weight of the compound. More preferably, the isolated sample contains at least 80% by weight of the compound. Even more preferably, the isolated sample contains at least 90% by weight of the compound. Most preferably, the isolated sample contains at least 95% by weight of the compound. The purity of an isolated sample of a compound of the present invention may be assessed by a number of methods or a combination of them; e.g., thin-layer, preparative or flash chromatography, mass spectrometry, HPLC, NMR analysis, and the like.
The term “heteroatom” is art-recognized and refers to an atom of any element other than carbon or hydrogen. Illustrative heteroatoms include boron, nitrogen, oxygen, phosphorus, sulfur and selenium.
The term “alkyl” is art-recognized, and includes saturated aliphatic groups, including straight-chain alkyl groups, branched-chain alkyl groups, cycloalkyl (alicyclic) groups, alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In certain embodiments, a straight chain or branched chain alkyl has about 30 or fewer carbon atoms in its backbone (e.g., C1-C30 for straight chain, C3-C30 for branched chain), and alternatively, about 20 or fewer. Likewise, cycloalkyls have from about 3 to about 10 carbon atoms in their ring structure, and alternatively about 5, 6 or 7 carbons in the ring structure.
Unless the number of carbons is otherwise specified, “lower alkyl” refers to an alkyl group, as defined above, but having from one to about ten carbons, alternatively from one to about six carbon atoms in its backbone structure. Likewise, “lower alkenyl” and “lower alkynyl” have similar chain lengths.
The term “aralkyl” is art-recognized and refers to an alkyl group substituted with an aryl group (e.g., an aromatic or heteroaromatic group).
The terms “alkenyl” and “alkynyl” are art-recognized and refer to unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double or triple bond respectively.
The term “aryl” is art-recognized and refers to 5-, 6- and 7-membered single-ring aromatic groups that may include from zero to four heteroatoms, for example, benzene, naphthalene, anthracene, pyrene, pyrrole, furan, thiophene, imidazole, oxazole, thiazole, triazole, pyrazole, pyridine, pyrazine, pyridazine and pyrimidine, and the like. Those aryl groups having heteroatoms in the ring structure may also be referred to as “aryl heterocycles” or “heteroaromatics.” The aromatic ring may be substituted at one or more ring positions with such substituents as described above, for example, halogen, azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, sulfonamido, ketone, aldehyde, ester, heterocyclyl, aromatic or heteroaromatic moieties, —CF3, —CN, or the like. The term “aryl” also includes polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings (the rings are “fused rings”) wherein at least one of the rings is aromatic, e.g., the other cyclic rings may be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls.
The terms ortho, meta and para are art-recognized and refer to 1,2-, 1,3- and 1,4-disubstituted benzenes, respectively. For example, the names 1,2-dimethylbenzene and ortho-dimethylbenzene are synonymous.
The terms “heterocyclyl”, “heteroaryl”, or “heterocyclic group” are art-recognized and refer to 3- to about 10-membered ring structures, alternatively 3- to about 7-membered rings, whose ring structures include one to four heteroatoms. Heterocycles may also be polycycles. Heterocyclyl groups include, for example, thiophene, thianthrene, furan, pyran, isobenzofuran, chromene, xanthene, phenoxanthene, pyrrole, imidazole, pyrazole, isothiazole, isoxazole, pyridine, pyrazine, pyrimidine, pyridazine, indolizine, isoindole, indole, indazole, purine, quinolizine, isoquinoline, quinoline, phthalazine, naphthyridine, quinoxaline, quinazoline, cinnoline, pteridine, carbazole, carboline, phenanthridine, acridine, pyrimidine, phenanthroline, phenazine, phenarsazine, phenothiazine, piperonyl, furazan, phenoxazine, pyrrolidine, oxolane, thiolane, oxazole, piperidine, piperazine, morpholine, lactones, lactams such as azetidinones and pyrrolidinones, sultams, sultones, and the like. The heterocyclic ring may be substituted at one or more positions with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, —CF3, —CN, or the like.
The term “optionally substituted” refers to a chemical group, such as alkyl, cycloalkyl aryl, and the like, wherein one or more hydrogen may be replaced with a substituent as described herein, including but not limited to halogen, azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, sulfonamido, ketone, aldehyde, ester, heterocyclyl, aromatic or heteroaromatic moieties, —CF3, —CN, or the like.
The terms “polycyclyl” or “polycyclic group” are art-recognized and refer to two or more rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are “fused rings”. Rings that are joined through non-adjacent atoms are termed “bridged” rings. Each of the rings of the polycycle may be substituted with such substituents as described above, as for example, halogen, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, ketone, aldehyde, ester, a heterocyclyl, an aromatic or heteroaromatic moiety, —CF3, —CN, or the like.
The term “carbocycle” is art-recognized and refers to an aromatic or non-aromatic ring in which each atom of the ring is carbon.
The term “nitro” is art-recognized and refers to —NO2; the term “halogen” is art-recognized and refers to —F, —Cl, —Br or —I; the term “sulfhydryl” is art-recognized and refers to —SH; the term “hydroxyl” means —OH; and the term “sulfonyl” is art-recognized and refers to —SO2−. “Halide” designates the corresponding anion of the halogens, and “pseudohalide” has the definition set forth on 560 of Advanced Inorganic Chemistry by Cotton and Wilkinson.
The terms “amine” and “amino” are art-recognized and refer to both unsubstituted and substituted amines, e.g., a moiety that may be represented by the general formulas:
wherein R50, R51 and R52 each independently represent a hydrogen, an alkyl, an alkenyl, —(CH2)m—R61, or R50 and R51, taken together with the N atom to which they are attached complete a heterocycle having from 4 to 8 atoms in the ring structure; R61 represents an aryl, a cycloalkyl, a cycloalkenyl, a heterocycle or a polycycle; and m is zero or an integer in the range of 1 to 8. In other embodiments, R50 and R51 (and optionally R52) each independently represent a hydrogen, an alkyl, an alkenyl, or —(CH2)m—R61. Thus, the term “alkylamine” includes an amine group, as defined above, having a substituted or unsubstituted alkyl attached thereto, i.e., at least one of R50 and R51 is an alkyl group.
The term “acylamino” is art-recognized and refers to a moiety that may be represented by the general formula:
wherein R50 is as defined above, and R54 represents a hydrogen, an alkyl, an alkenyl or —(CH2)m—R61, where m and R61 are as defined above.
The term “amido” is art recognized as an amino-substituted carbonyl and includes a moiety that may be represented by the general formula:
wherein R50 and R51 are as defined above. Certain embodiments of the amide in the present invention will not include imides which may be unstable.
The term “alkylthio” refers to an alkyl group, as defined above, having a sulfur radical attached thereto. In certain embodiments, the “alkylthio” moiety is represented by one of —S-alkyl, —S-alkenyl, —S-alkynyl, and —S—(CH2)m—R61, wherein m and R61 are defined above. Representative alkylthio groups include methylthio, ethyl thio, and the like.
The term “carboxyl” is art recognized and includes such moieties as may be represented by the general formulas:
wherein X50 is a bond or represents an oxygen or a sulfur, and R55 and R56 represents a hydrogen, an alkyl, an alkenyl, —(CH2)m—R61 or a pharmaceutically acceptable salt, R56 represents a hydrogen, an alkyl, an alkenyl or —(CH2)m—R61, where m and R61 are defined above. Where X50 is an oxygen and R55 or R56 is not hydrogen, the formula represents an “ester”. Where X50 is an oxygen, and R55 is as defined above, the moiety is referred to herein as a carboxyl group, and particularly when R55 is a hydrogen, the formula represents a “carboxylic acid”. Where X50 is an oxygen, and R56 is hydrogen, the formula represents a “formate”. In general, where the oxygen atom of the above formula is replaced by sulfur, the formula represents a “thiolcarbonyl” group. Where X50 is a sulfur and R55 or R56 is not hydrogen, the formula represents a “thiolester.” Where X50 is a sulfur and R55 is hydrogen, the formula represents a “thiolcarboxylic acid.” Where X50 is a sulfur and R56 is hydrogen, the formula represents a “thiolformate.” On the other hand, where X50 is a bond, and R55 is not hydrogen, the above formula represents a “ketone” group. Where X50 is a bond, and R55 is hydrogen, the above formula represents an “aldehyde” group.
The term “carbamoyl” refers to —O(C═O)NRR′, where R and R′ are independently H, aliphatic groups, aryl groups or heteroaryl groups.
The term “oxo” refers to a carbonyl oxygen (═O).
The terms “oxime” and “oxime ether” are art-recognized and refer to moieties that may be represented by the general formula:
wherein R75 is hydrogen, alkyl, cycloalkyl, alkenyl, alkynyl, aryl, aralkyl, or —(CH2)m—R61. The moiety is an “oxime” when R is H; and it is an “oxime ether” when R is alkyl, cycloalkyl, alkenyl, alkynyl, aryl, aralkyl, or —(CH2)m—R61.
The terms “alkoxyl” or “alkoxy” are art-recognized and refer to an alkyl group, as defined above, having an oxygen radical attached thereto. Representative alkoxyl groups include methoxy, ethoxy, propyloxy, tert-butoxy and the like. An “ether” is two hydrocarbons covalently linked by an oxygen. Accordingly, the substituent of an alkyl that renders that alkyl an ether is or resembles an alkoxyl, such as may be represented by one of —O-alkyl, —O-alkenyl, —O-alkynyl, —O—(CH2)m—R61, where m and R61 are described above.
The term “sulfonate” is art recognized and refers to a moiety that may be represented by the general formula:
in which R57 is an electron pair, hydrogen, alkyl, cycloalkyl, or aryl.
The term “sulfate” is art recognized and includes a moiety that may be represented by the general formula:
in which R57 is as defined above.
The term “sulfonamido” is art recognized and includes a moiety that may be represented by the general formula:
in which R50 and R56 are as defined above.
The term “sulfamoyl” is art-recognized and refers to a moiety that may be represented by the general formula:
in which R50 and R51 are as defined above.
The term “sulfonyl” is art-recognized and refers to a moiety that may be represented by the general formula:
in which R58 is one of the following: hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl or heteroaryl.
The term “sulfoxido” is art-recognized and refers to a moiety that may be represented by the general formula:
in which R58 is defined above.
The term “phosphoryl” is art-recognized and may in general be represented by the formula:
wherein Q50 represents S or O, and R59 represents hydrogen, a lower alkyl or an aryl. When used to substitute, e.g., an alkyl, the phosphoryl group of the phosphorylalkyl may be represented by the general formulas:
wherein Q50 and R59, each independently, are defined above, and Q51 represents O, S or N. When Q50 is S, the phosphoryl moiety is a “phosphorothioate”.
The term “phosphoramidite” is art-recognized and may be represented in the general formulas:
wherein Q51, R50, R51 and R59 are as defined above.
The term “phosphonamidite” is art-recognized and may be represented in the general formulas:
wherein Q51, R50, R51 and R59 are as defined above, and R60 represents a lower alkyl or an aryl.
Analogous substitutions may be made to alkenyl and alkynyl groups to produce, for example, aminoalkenyls, aminoalkynyls, amidoalkenyls, amidoalkynyls, iminoalkenyls, iminoalkynyls, thioalkenyls, thioalkynyls, carbonyl-substituted alkenyls or alkynyls.
The definition of each expression, e.g., alkyl, m, n, and the like, when it occurs more than once in any structure, is intended to be independent of its definition elsewhere in the same structure.
The terms triflyl, tosyl, mesyl, and nonaflyl are art-recognized and refer to trifluoromethanesulfonyl, p-toluenesulfonyl, methanesulfonyl, and nonafluorobutanesulfonyl groups, respectively. The terms triflate, tosylate, mesylate, and nonaflate are art-recognized and refer to trifluoromethanesulfonate ester, p-toluenesulfonate ester, methanesulfonate ester, and nonafluorobutanesulfonate ester functional groups and molecules that contain said groups, respectively.
The abbreviations Me, Et, Ph, Tf, Nf, Ts, and Ms represent methyl, ethyl, phenyl, trifluoromethanesulfonyl, nonafluorobutanesulfonyl, p-toluenesulfonyl and methanesulfonyl, respectively. A more comprehensive list of the abbreviations utilized by organic chemists of ordinary skill in the art appears in the first issue of each volume of the Journal of Organic Chemistry; this list is typically presented in a table entitled “Standard List of Abbreviations.”
Certain compounds contained in compositions of the present invention may exist in particular geometric or stereoisomeric forms. In addition, polymers of the present invention may also be optically active. The present invention contemplates all such compounds, including cis- and trans-isomers, E- and Z-isomers, R- and S-enantiomers, diastereomers, (D)-isomers, (L)-isomers, the racemic mixtures thereof, and other mixtures thereof, as falling within the scope of the invention. Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in this invention.
If, for instance, a particular enantiomer of compound of the present invention is desired, it may be prepared by asymmetric synthesis, or by derivation with a chiral auxiliary, where the resulting diastereomeric mixture is separated and the auxiliary group cleaved to provide the pure desired enantiomers. Alternatively, where the molecule contains a basic functional group, such as amino, or an acidic functional group, such as carboxyl, diastereomeric salts are formed with an appropriate optically-active acid or base, followed by resolution of the diastereomers thus formed by fractional crystallization or chromatographic means well known in the art, and subsequent recovery of the pure enantiomers.
It will be understood that “substitution” or “substituted with” includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
The term “substituted” is also contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds. Illustrative substituents include, for example, those described herein above. The permissible substituents may be one or more and the same or different for appropriate organic compounds. For purposes of this invention, the heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. This invention is not intended to be limited in any manner by the permissible substituents of organic compounds.
The phrase “protecting group” as used herein means temporary substituents which protect a potentially reactive functional group from undesired chemical transformations. Examples of such protecting groups include esters of carboxylic acids, silyl ethers of alcohols, and acetals and ketals of aldehydes and ketones, respectively. Examples of nitrogen protecting groups include an amide (—NRC(═O)R) or a urethane (—NRC(═O)OR), for example, as: a methyl amide (—NHC(═O)CH3); a benzyloxy amide (—NHC(═O)OCH2C6H5NHCbz); as a t-butoxy amide (—NHC(═O)OC(CH3)3, —NHBoc); a 2-biphenyl-2-propoxy amide (—NHC(═O)OC(CH3)2C6H4C6H5NHBoc), as a 9-fluorenylmethoxy amide (—NHFmoc), as a 6-nitroveratryloxy amide (—NHNvoc), as a 2-trimethylsilylethyloxy amide (—NHTeoc), as a 2,2,2-trichloroethyloxy amide (—NHTroc), as an allyloxy amide (—NHAlloc), as a 2-(phenylsulfonyl)ethyloxy amide (—NHPsec); or, in suitable cases (e.g., cyclic amines), as a nitroxide radical. The field of protecting group chemistry has been reviewed (Greene, T. W.; Wuts, P. G. M. Protective Groups in Organic Synthesis, 2nd ed.; Wiley: New York, 1991). Protected forms of the inventive compounds are included within the scope of this invention.
The term “pharmaceutically acceptable salt” or “salt” refers to a salt of one or more compounds. Suitable pharmaceutically acceptable salts of compounds include acid addition salts, such as those formed with mineral acids such as hydrochloric acid and hydrobromic acid, and also those formed with organic acids such as maleic acid. For example, acids commonly employed to form pharmaceutically acceptable salts include inorganic acids such as hydrogen bisulfide, hydrochloric, hydrobromic, hydroiodic, sulfuric and phosphoric acid, as well as organic acids such as para-toluenesulfonic, salicylic, tartaric, bitartaric, ascorbic, maleic, besylic, fumaric, gluconic, glucuronic, formic, glutamic, methanesulfonic, ethanesulfonic, benzenesulfonic, lactic, oxalic, para-bromophenylsulfonic, carbonic, succinic, citric, benzoic and acetic acid, and related inorganic and organic acids. Such pharmaceutically acceptable salts thus include sulfate, pyrosulfate, bisulfate, sulfite, bisulfite, phosphate, monohydrogenphosphate, dihydrogenphosphate, metaphosphate, pyrophosphate, chloride, bromide, iodide, acetate, propionate, decanoate, caprylate, acrylate, formate, isobutyrate, caprate, heptanoate, propiolate, oxalate, malonate, succinate, suberate, sebacate, fumarate, maleate, butyne-1,4-dioate, hexyne-1,6-dioate, benzoate, chlorobenzoate, methylbenzoate, dinitrobenzoate, hydroxybenzoate, methoxybenzoate, phthalate, terephathalate, sulfonate, xylenesulfonate, phenylacetate, phenylpropionate, phenylbutyrate, citrate, lactate, β-hydroxybutyrate, glycolate, maleate, tartrate, methanesulfonate, propanesulfonate, naphthalene-1-sulfonate, naphthalene-2-sulfonate, mandelate and the like.
Where the compounds carry one or more acidic moieties, pharmaceutically acceptable salts may be formed by treatment of a solution of the compound with a solution of a pharmaceutically acceptable base. Suitable bases for forming pharmaceutically acceptable salts with acidic functional groups include, but are not limited to, hydroxides and carbonates of alkali metals such as sodium, potassium, and lithium; alkaline earth metal such as calcium and magnesium; and other metals, such as aluminum and zinc. Suitable bases also include ammonia, and organic amines, such as unsubstituted or hydroxy-substituted mono-, di-, or trialkylamines; dicyclohexylamine; tributyl amine; pyridine; N-methyl,N-ethylamine; diethylamine; triethylamine; mono-, bis-, or tris-(2-hydroxy-lower alkyl amines), such as mono-, bis-, or tris-(2-hydroxyethyl)amine, 2-hydroxy-tert-butylamine, or tris-(hydroxymethyl)methylamine, N,N-di alkyl-N-(hydroxy alkyl)-amines, such as N,N-dimethyl-N-(2-hydroxyethyl)amine, or tri-(2-hydroxyethyl)amine; N-methyl-D-glucamine; and amino acids such as arginine, lysine, and the like.
Certain compounds of the invention and their salts may exist in more than one crystalline form (i.e., polymorph); the present invention includes each of the crystal forms and mixtures thereof.
Certain compounds of the invention and their salts may also exist in the form of solvates, for example hydrates, and the present invention includes each solvate and mixtures thereof.
Certain compounds of the invention may contain one or more chiral centers, and exist in different optically active forms. When compounds of the invention contain one chiral center, the compounds exist in two enantiomeric forms and the present invention includes both enantiomers and mixtures of enantiomers, such as racemic mixtures thereof. The enantiomers may be resolved by methods known to those skilled in the art; for example, enantiomers may be resolved by formation of diastereoisomeric salts which may be separated, for example, by crystallization; formation of diastereoisomeric derivatives or complexes which may be separated, for example, by crystallization, gas-liquid or liquid chromatography; selective reaction of one enantiomer with an enantiomer-specific reagent, for example, via enzymatic esterification; or gas-liquid or liquid chromatography in a chiral environment, for example, on a chiral support; suitable include chiral supports (e.g., silica with a bound chiral ligand) or in the presence of a chiral solvent. Where the desired enantiomer is converted into another chemical entity by one of the separation procedures described above, a further step may be used to liberate the desired purified enantiomer. Alternatively, specific enantiomers may be synthesized by asymmetric synthesis using optically active reagents, substrates, catalysts or solvents, or by converting one enantiomer into the other by asymmetric transformation.
When a compound of the invention contains more than one chiral center, it may exist in diastereoisomeric forms. The diastereoisomeric compounds may be separated by methods known to those skilled in the art (for example, chromatography or crystallization) and the individual enantiomers may be separated as described above. The present invention includes the various diastereoisomers of compounds of the invention, and mixtures thereof. Compounds of the invention may exist in different tautomeric forms or as different geometric isomers, and the present invention includes each tautomer and/or geometric isomer of compounds of the invention, and mixtures thereof. For example, any olefins present in the compounds may exist as either the E- or Z-geometric isomers or a mixture thereof unless stated otherwise. Compounds of the invention may exist in zwitterionic form. The present invention includes each zwitterionic form of compounds of the invention, and mixtures thereof.
As used herein the term “pro-drug” refers to an agent, which is converted into the parent drug in vivo by some physiological chemical process (e.g., a prodrug on being brought to the physiological pH is converted to the desired drug form). Pro-drugs are often useful because, in some situations, they may be easier to administer than the parent drug. They may, for instance, be bioavailable by oral administration whereas the parent drug is not. The prodrug may also have improved solubility in pharmacological compositions over the parent drug. An example, without limitation, of a pro-drug would be a compound of the present invention wherein it is administered as an ester (the “pro-drug”) to facilitate transmittal across a cell membrane where water solubility is not beneficial, but then it is metabolically hydrolyzed to the carboxylic acid once inside the cell where water solubility is beneficial. Pro-drugs have many useful properties. For example, a pro-drug may be more water soluble than the ultimate drug, thereby facilitating intravenous administration of the drug. A pro-drug may also have a higher level of oral bioavailability than the ultimate drug. After administration, the prodrug is enzymatically or chemically cleaved to deliver the ultimate drug in the blood or tissue.
Exemplary pro-drugs release an amine of a compound of the invention wherein the free hydrogen of an amine or alcohol is replaced by (C1-C6)alkanoyloxymethyl, 1-((C1-C6)alkanoyloxy)ethyl, 1-methyl-1-((C1-C6)alkanoyloxy)ethyl, (C1-C6)alkoxycarbonyloxymethyl, N—(C1-C6)alkoxycarbonylamino-methyl, succinoyl, (C1-C6)alkanoyl, α-amino(C1-C4)alkanoyl, arylactyl and α-aminoacyl, or α-aminoacyl-α-aminoacyl wherein said α-aminoacyl moieties are independently any of the naturally occurring L-amino acids found in proteins, —P(O)(OH)2, —P(O)(O(C1-C6)alkyl)2 or glycosyl (the radical resulting from detachment of the hydroxyl of the hemiacetal of a carbohydrate).
Other exemplary pro-drugs upon cleavage release a corresponding free acid, and such hydrolyzable ester-forming residues of the compounds of this invention include but are not limited to carboxylic acid substituents (e.g., —(CH2)C(O)OH or a moiety that contains a carboxylic acid) wherein the free hydrogen is replaced by (C1-C4)alkyl, (C2-C12)alkanoyloxymethyl, (C4-C9)1-(alkanoyloxy)ethyl, 1-methyl-1-(alkanoyloxy)-ethyl having from 5 to 10 carbon atoms, alkoxycarbonyloxymethyl having from 3 to 6 carbon atoms, 1-(alkoxycarbonyloxy)ethyl having from 4 to 7 carbon atoms, 1-methyl-1-(alkoxycarbonyloxy)ethyl having from 5 to 8 carbon atoms, N-(alkoxycarbonyl)aminomethyl having from 3 to 9 carbon atoms, 1-(N-(alkoxycarbonyl)amino)ethyl having from 4 to 10 carbon atoms, 3-phthalidyl, 4-crotonolactonyl, gamma-butyrolacton-4-yl, di-N,N—(C1-C2)alkylamino(C2-C3)alkyl (such as β-dimethylaminoethyl), carbamoyl-(C1-C2)alkyl, N,N-di(C1-C2)-alkylcarbamoyl-(C1-C2)alkyl and piperidino-, pyrrolidino- or morpholino(C2-C3)alkyl.
The term “subject” as used herein, refers to an animal, typically a mammal or a human, that will be or has been the object of treatment, observation, and/or experiment. When the term is used in conjunction with administration of a compound or drug, then the subject has been the object of treatment, observation, and/or administration of the compound or drug.
The terms “co-administration” and “co-administering” refer to both concurrent administration (administration of two or more therapeutic agents at the same time) and time varied administration (administration of one or more therapeutic agents at a time different from that of the administration of an additional therapeutic agent or agents), as long as the therapeutic agents are present in the patient to some extent at the same time.
The term “therapeutically effective amount” as used herein, means that amount of active compound or pharmaceutical agent that elicits a biological or medicinal response in a cell culture, tissue system, animal, or human that is being sought by a researcher, veterinarian, clinician, or physician, which includes alleviation of the symptoms of the disease, condition, or disorder being treated.
The term “composition” is intended to encompass a product comprising the specified ingredients in the specified amounts, as well as any product that results, directly or indirectly, from combinations of the specified ingredients in the specified amounts.
The term “pharmaceutically acceptable carrier” refers to a medium that is used to prepare a desired dosage form of a compound. A pharmaceutically acceptable carrier can include one or more solvents, diluents, or other liquid vehicles; dispersion or suspension aids; surface active agents; isotonic agents; thickening or emulsifying agents; preservatives; solid binders; lubricants; and the like. Remington's Pharmaceutical Sciences, Fifteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1975) and Handbook of Pharmaceutical Excipients, Third Edition, A. H. Kibbe ed. (American Pharmaceutical Assoc. 2000), disclose various carriers used in formulating pharmaceutical compositions and known techniques for the preparation thereof.
Compounds
An aspect of the invention relates to a compound of formula 1:
or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
wherein any one of the aforementioned alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl, and heterocyclylalkyl may be optionally substituted.
In one embodiment, W and X are oxygen.
In one embodiment, Z1 and Z2 are nitrogen; and Z3 is C—R20.
In one embodiment, Z1, Z2 and Z3 are nitrogen.
In one embodiment, Z1 is nitrogen; and Z2 and Z3 are each C—R20.
In one embodiment, Z2 is nitrogen; and Z1 and Z3 are each C—R20.
In one embodiment, R1 is hydrogen.
In one embodiment, R1 is selected from the group consisting of alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, and —[C(R4)2]p—R5.
In one embodiment, W and X are oxygen, Z1 and Z2 are each nitrogen, Z3 is C—R20 and R1 is hydrogen.
In one embodiment, R2 and R3 are joined together to form an optionally substituted heterocyclic ring.
In one embodiment, the optionally substituted heterocyclic ring is selected from the group consisting of piperazinyl, homopiperizinyl, pyrrolidinyl, piperidinyl, homopiperidinyl, morpholinyl, 1,4-diazepan-5-onyl and quinolinyl.
In one embodiment, R2 and R3 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, —[C(R4)2]p—R5, —COR6, —C(O)OR6, —SO2(R6), —C(O)N(R6)(R7), and —SO2N(R6)(R7), wherein the alkyl, alkenyl, alkynyl, aryl, heteroaryl, and heterocyclyl may be optionally substituted.
In one embodiment, R2 is —[C(R4)2]p—R5, and R3 is selected from the group consisting of alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, —COR6, —C(O)OR6, —SO2(R6), —C(O)N(R6)(R7), and —SO2N(R6)(R7), wherein the alkyl, alkenyl, alkynyl, aryl, heteroaryl, and heterocyclyl may be optionally substituted.
In one embodiment, R5 is aryl or heteroaryl, each of which may be optionally substituted.
In one embodiment, R5 is —N(R8)(R9).
In one embodiment, R4 is hydrogen.
In one embodiment, R20 is selected from the group consisting of alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, halo, haloalkyl, trifluoromethyl, carboxyl, alkoxycarbonyl, acyl, nitro, amido, acylamino, sulfonamido, —[C(R4)2]p—R5; NR14R15, OR16, and SR16.
In one embodiment, R20 is hydrogen.
An aspect of the invention relates to compound of formula 2:
or a pharmaceutically acceptable salt thereof, wherein independently for each occurrence:
wherein any one of the aforementioned alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl, and heterocyclylalkyl may be optionally substituted.
In one embodiment, R1 is hydrogen.
In one embodiment, R20 is selected from the group consisting of hydrogen, alkyl, trifluoromethyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, —[C(R4)2]p—R5, NR14R15, OR16, and SR16.
In one embodiment, R20 is hydrogen.
In one embodiment, R2 and R3 are joined together to form an optionally substituted heterocyclic ring.
In one embodiment, R2 and R3 are joined together to form an optionally substituted heterocyclic ring selected from the group consisting of:
wherein, independently for each occurrence:
wherein any one of the aforementioned alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, aralkyl, heteroaralkyl, and heterocyclylalkyl may be optionally substituted.
In one embodiment, R10 is selected from the group consisting of hydrogen, alkyl, aryl, heteroaryl, heterocyclyl, —[C(R4)2]p—R5, —COR12, —C(O)OR12, and —SO2(R12);
wherein any one of the aforementioned alkyl, aryl, heteroaryl, and heterocyclyl may be optionally substituted.
In one embodiment, n is 0.
In one embodiment, n is 1.
In one embodiment, R11 is selected from the group consisting of alkyl, heterocyclyl, cyano, hydroxyalkyl, —N(R17)(R18), —CON(R17)(R18), and —[C(R4)2]p—R5;
wherein any of the aforementioned alkyl and heterocyclyl may be optionally substituted.
In one embodiment, R2 and R3 are joined together to form an optionally substituted heterocyclic ring of the formula:
In one embodiment, n is 0 or 1.
In one embodiment, R2 and R3 are joined together to form an optionally substituted heterocyclic ring of the formula:
In one embodiment, R2 and R3 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclyl, —[C(R4)2]p—R5, —COR6, —C(O)OR6, —SO2(R6), —C(O)N(R6)(R7), and —SO2N(R6)(R7), wherein the alkyl, alkenyl, alkynyl, aryl, heteroaryl, and heterocyclyl may be optionally substituted.
In one embodiment, R3 is —[C(R4)2]p—R5.
In one embodiment, R2 is optionally substituted alkyl.
In one embodiment, R4 is hydrogen.
In one embodiment, R4 is hydroxy.
In one embodiment, R5 is aryl, heteroaryl, heterocyclyl, each of which may be optionally substituted.
In one embodiment, p is 1, 2 or 3.
In one embodiment, R5 is selected from the group consisting of —N(R8)(R9), —N(R8)COR9, —N(R8)C(O)OR9, —N(R8)SO2(R9), —CON(R8)(R9), —OC(O)N(R8)—(R9), —SO2N(R8)(R9), —OC(O)OR8, —COOR9, —C(O)N(OH)(R8), —OS(O)2OR8, —S(O)2OR8, —S(O)2R8, —OR8, —CORS, —OP(O)(OR8)(OR8), —P(O)(OR8)(OR8) and —N(R8)P(O)(OR9)(OR9).
In one embodiment, R5 is —N(R8)(R9).
An aspect of the invention relates to a compound, or a pharmaceutically acceptable salt thereof, selected from the group consisting of:
An aspect of the invention relates to a compound, or a pharmaceutically acceptable salt thereof, selected from the group consisting of:
Any one of the aforementioned compounds may exist as the E-geometric isomer, the Z-geometric isomer, or mixtures thereof. For example, in one embodiment,
in the aforementioned structures represents the E-isomer of the particular compound. In another embodiment,
represents the Z-isomer of the particular compound. In yet another embodiment,
represents a mixture of E and Z isomers of the particular compound.
In one embodiment, any one of the aforementioned compounds is an inhibitor of CK1γ1, CK1γ2, or CK1γ3.
In one embodiment, any one of the aforementioned compounds is an inhibitor of CK2.
In one embodiment, any one of the aforementioned compounds is an inhibitor of the Wnt pathway.
In one embodiment, any one of the aforementioned compounds is an inhibitor of the JAK/STAT pathway.
In one embodiment, any one of the aforementioned compounds is an inhibitor of the mTOR pathway.
In one embodiment, any one of the aforementioned compounds is a mediator of Pgp degradation and/or drug efflux.
In one embodiment, any one of the aforementioned compounds is an inhibitor of the TGFβ pathway.
In some embodiments, the compound has an IC50 of less than 5000 nM for CK1γ1, CK1γ2, or CK1γ3.
In some embodiments, the compound has an IC50 of less than 1000 nM for CK1γ1, CK1γ2, or CK1γ3.
In some embodiments, the compound has an IC50 of less than 500 nM for CK1γ1, CK1γ2, or CK1γ3.
In one embodiment, any one of the aforementioned compounds is an inhibitor of CK2.
In one embodiment, the compound has an IC50 of less than 5000 nM for CK2.
In one embodiment, the compound has an IC50 of less than 1000 nM for CK2.
In one embodiment, the compound has an IC50 of less than 500 nM for CK2.
In one embodiment, any on of the aforementioned compounds is an inhibitor of PIM1, PIM2, or PIM3.
In one embodiment, the compound has an IC50 of less than 5000 nM for PIM1, PIM2 or PIM3.
In one embodiment, the compound has an IC50 of less than 1000 nM for PIM1, PIM2 or PIM3.
In one embodiment, the compound has an IC50 of less than 500 nM for PIM1, PIM2 or PIM3.
General Synthetic Schemes
General synthetic schemes that were utilized to prepare compounds disclosed in this application are described below. For example, compounds of the invention may be prepared as shown in Scheme I:
Alternatively, the compounds of the invention can be made as shown in Scheme II:
Yet another method of making the compounds disclosed herein is depicted in Scheme III:
Prophetic Embodiments
Certain compounds of the invention could be made in accordance with the above schemes by reacting an amine (Reactant A) with the hydantoin core (Reactant B). Non-limiting prophetic examples of Reactant A and Reactant B are shown in Table 1 and Table 2, respectively.
Additional prophetic embodiments of the invention that may be made in accordance with the above reaction schemes using Reactants A and B are listed in Table 3. The geometric isomers listed in Table 3 are believed to reflect the actual geometry of the prophetic compounds if they were to be made; however, final structural assignments may only be made if the compounds are synthesized and subjected to appropriate 2D NMR experiments. Further, although the compounds are listed as the “Z” geometric isomer, both the E and Z geometric isomers and mixtures thereof are contemplated.
In addition, it may be convenient or desirable to prepare, purify, and/or handle the active compound in a chemically protected form. The term “chemically protected form,” as used herein, pertains to a compound in which one or more reactive functional groups are protected from undesirable chemical reactions (i.e., they have been modified with a protecting group).
By protecting a reactive functional group, reactions involving other unprotected reactive functional groups can be performed without affecting the protected group; the protecting group may be removed, usually in a subsequent step, without substantially affecting the remainder of the molecule. See, for example, Protective Groups in Organic Synthesis (T. Green and P. Wuts, Wiley, 1991), and Protective Groups in Organic Synthesis (T. Green and P. Wuts; 3rd Edition; John Wiley and Sons, 1999).
For example, a hydroxy group may be protected as an ether (—OR) or an ester (—OC(═O)R), for example, as: a t-butyl ether; a benzyl, benzhydryl (diphenylmethyl), or trityl (triphenylmethyl)ether; a trimethylsilyl or t-butyldimethylsilyl ether; or an acetyl ester (—OC(═O)CH3, —OAc).
For example, an aldehyde or ketone group may be protected as an acetal or ketal, respectively, in which the carbonyl group (C(═O)) is converted to a diether (C(OR)2), by reaction with, for example, a primary alcohol. The aldehyde or ketone group is readily regenerated by hydrolysis using a large excess of water in the presence of acid.
For example, an amine group may be protected, for example, as an amide (—NRC(═O)R) or a urethane (—NRC(═O)OR), for example, as: a methyl amide (—NHC(═O)CH3); a benzyloxy amide (—NHC(═O)OCH2C6H5NHCbz); as a t-butoxy amide (—NHC(═O)OC(CH3)3, —NHBoc); a 2-biphenyl-2-propoxy amide (—NHC(═O)OC(CH3)2C6H4C6H5NHBoc), as a 9-fluorenylmethoxy amide (—NHFmoc), as a 6-nitroveratryloxy amide (—NHNvoc), as a 2-trimethylsilylethyloxy amide (—NHTeoc), as a 2,2,2-trichloroethyloxy amide (—NHTroc), as an allyloxy amide (—NHAlloc), as a 2-(phenylsulfonyl)ethyloxy amide (—NHPsec); or, in suitable cases (e.g., cyclic amines), as a nitroxide radical.
For example, a carboxylic acid group may be protected as an ester or an amide, for example, as: a benzyl ester; a t-butyl ester; a methyl ester; or a methyl amide.
For example, a thiol group may be protected as a thioether (—SR), for example, as: a benzyl thioether; or an acetamidomethyl ether (—SCH2NHC(═O)CH3).
Pharmaceutical Compositions
One or more compounds of this invention can be administered to a mammal by themselves or in pharmaceutical compositions where they are mixed with suitable carriers or excipient(s) at doses to treat or ameliorate a disease or condition as described herein. Mixtures of these compounds can also be administered to the patient as a simple mixture or in suitable formulated pharmaceutical compositions. For example, one aspect of the invention relates to pharmaceutical composition comprising a therapeutically effective dose of a compound of formula I, or a pharmaceutically acceptable salt, solvate, enantiomer or stereoisomer thereof; and a pharmaceutically acceptable diluent or carrier.
Techniques for formulation and administration of the compounds of the instant application may be found in references well known to one of ordinary skill in the art, such as “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., latest edition.
Suitable routes of administration may, for example, include oral, eyedrop, rectal, transmucosal, topical, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
Alternatively, one may administer a compound in a local rather than a systemic manner, for example, via injection of the compound directly into an edematous site, often in a depot or sustained release formulation.
Furthermore, one may administer a compound in a targeted drug delivery system, for example, in a liposome coated with endothelial-cell-specific antibody.
The pharmaceutical compositions of the present invention may be manufactured, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
For injection, the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants are used in the formulation appropriate to the barrier to be permeated. Such penetrants are generally known in the art.
For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained by combining the active compound with a solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients include fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added.
For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.
For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
The compounds can be formulated for parenteral administration by injection, e.g., bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
Alternatively, the active ingredient may be in powder form for reconstitution before use with a suitable vehicle, e.g., sterile pyrogen-free water.
The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.
In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example, subcutaneously or intramuscularly or by intramuscular injection). Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives (for example, as a sparingly soluble salt).
Alternatively, other delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are examples of delivery vehicles or carriers for hydrophobic drugs. Certain organic solvents such as dimethysulfoxide also may be employed. Additionally, the compounds may be delivered using a sustained-release system, such as semi-permeable matrices of solid hydrophobic polymers containing the therapeutic agent. Various sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein stabilization may be employed.
The pharmaceutical compositions may also comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers, such as polyethylene glycols.
Methods of Treatment
Provided herein are methods of modulating the activity of CK1 and subtypes thereof, CK2, the Wnt pathway, and/or the TGFβ pathway. Also provided herein are methods of treating or preventing conditions and diseases the course of which can be influenced by modulating the activity of CK1 (e.g., CK1γ), CK2, the Wnt pathway, and/or the TGFβ pathway. Such methods typically comprise administering to a subject in need thereof a therapeutically effective amount of a compound or composition of the invention.
Also provided herein are methods of modulating the activity of PIM, such as PIM 1, PIM 2 or PIM 3, the JAK/STAT pathway, and/or the mTOR pathway, and/or Pgp. Also provided herein are methods of treating or preventing conditions and diseases, the course of which can be influenced by modulating the activity of the PIMs, the JAK/STAT pathway, and/or the mTOR pathway, and/or Pgp. Such methods typically comprise administering to a subject in need thereof a therapeutically effective amount of a compound or composition of the invention.
Various diseases, such as cancers, inflammation, and inflammatory diseases (e.g., osteoarthritis and rheumatoid arthritis), and neurological conditions (e.g., Alzheimer's disease) and neurodegeneration can be treated by administration of modulators of CK1 (e.g., CK1γ), CK2, the Wnt pathway and/or the TGFβ pathway. Bone-related diseases and conditions, including osteoporosis and bone formation, also can be treated by administration of modulators of CK1 (e.g., CK1γ), CK2, the Wnt pathway and/or the TGFβ pathway. Bone restoration can be facilitated by administration of modulators of CK1 (e.g., CK1γ), CK2, the Wnt pathway and/or the TGFβ pathway. Additional conditions that can be treated by administration of modulators of CK1 (e.g., CK1γ), CK2, the Wnt pathway and/or the TGFβ pathway include hypoglycemia, metabolic syndrome and diabetes. Modulators of CK1 (e.g., CK1γ), CK2, the Wnt pathway and/or the TGFβ pathway are also useful for influencing apoptosis (e.g., increasing the rate of apoptosis in cancerous cells). Modulators of CK1 (e.g., CK1γ), CK2, the Wnt pathway and/or the TGFβ pathway are also useful in treatment or prevention of aberrant embryonic development.
Based at least on the fact that increased CK1γ has been found to be associated with certain cancers, a method for treating cancer in a subject comprises administering to the subject in need thereof a therapeutically effective amount of a compound that inhibits CK1γ. PIM1, PIM2, PIM3, the JAK/STAT pathway, and/or the mTOR pathway have also been found to be associated with certain cancers. Therefore, provided herein is a method for treating cancer comprising administering to a subject in need thereof a therapeutically effective amount of a compound that inhibits PIM1 and/or PIM2 and/or PIM3.
PIM1, PIM2, and PIM3 have also been associated with protecting Pgp from degradation, which can regulate drug efflux and drug resistance. Therefore, provided herein is a method for treating malignancies comprising administering to a subject in need thereof a therapeutically effective amount of a compound that inhibits PIM1 and/or PIM2 and/or PIM3 in conjunction with another drug, compound or material to abrogate resistance to the drug, compound or material.
The compounds described herein can be used for modulating cell proliferation, generally. Accordingly, diseases that may be treated include hyperproliferative diseases, such as benign cell growth and malignant cell growth.
Exemplary cancers that may be treated include leukemias, e.g., acute lymphoid leukemia and myeloid leukemia, and carcinomas, such as colorectal carcinoma and hepatocarcinoma. Other cancers include Acute Lymphoblastic Leukemia; Acute Lymphoblastic Leukemia; Acute Myeloid Leukemia; Acute Myeloid Leukemia; Adrenocortical Carcinoma Adrenocortical Carcinoma; AIDS-Related Cancers; AIDS-Related Lymphoma; Anal Cancer; Astrocytoma, Childhood Cerebellar; Astrocytoma, Childhood Cerebral; Basal Cell Carcinoma, see Skin Cancer (non-Melanoma); Bile Duct Cancer, Extrahepatic; Bladder Cancer; Bladder Cancer; Bone Cancer, osteosarcoma/Malignant Fibrous Histiocytoma; Brain Stem Glioma; Brain Tumor; Brain Tumor, Brain Stem Glioma; Brain Tumor, Cerebellar Astrocytoma; Brain Tumor, Cerebral Astrocytoma/Malignant Glioma; Brain Tumor, Ependymoma; Brain Tumor, Medulloblastoma; Brain Tumor, Supratentorial Primitive Neuroectodermal Tumors; Brain Tumor, Visual Pathway and Hypothalamic Glioma; Brain Tumor; Breast Cancer; Breast Cancer and Pregnancy; Breast Cancer; Breast Cancer, Male; Bronchial Adenomas/Carcinoids; Burkitt's Lymphoma; Carcinoid Tumor; Carcinoid Tumor, Gastrointestinal; Carcinoma of Unknown Primary; Central Nervous System Lymphoma, Primary; Cerebellar Astrocytoma; Cerebral Astrocytoma/Malignant Glioma; Cervical Cancer; Childhood Cancers; Chronic Lymphocytic Leukemia; Chronic Myelogenous Leukemia; Chronic Myeloproliferative Disorders; Colon Cancer; Colorectal Cancer; Cutaneous T-Cell Lymphoma, see Mycosis Fungoides and Sezary Syndrome; Endometrial Cancer; Ependymoma; Esophageal Cancer; Esophageal Cancer; Ewing's Family of Tumors; Extracranial Germ Cell Tumor; Extragonadal Germ Cell Tumor; Extrahepatic Bile Duct Cancer; Eye Cancer, Intraocular Melanoma; Eye Cancer, Retinoblastoma; Gallbladder Cancer; Gastric (Stomach) Cancer; Gastric (Stomach) Cancer; Gastrointestinal Carcinoid Tumor; Germ Cell Tumor, Extracranial; Germ Cell Tumor, Extragonadal; Germ Cell Tumor, Ovarian; Gestational Trophoblastic Tumor; Glioma; Glioma, Childhood Brain Stem; Glioma, Childhood Cerebral Astrocytoma; Glioma, Childhood Visual Pathway and Hypothalamic; Hairy Cell Leukemia; Head and Neck Cancer; Hematologic (Blood) Cancer, Hepatocellular (Liver) Cancer, Adult (Primary); Hepatocellular (Liver) Cancer, Childhood (Primary); Hodgkin's Lymphoma; Hodgkin's Lymphoma; Hodgkin's Lymphoma During Pregnancy; Hypopharyngeal Cancer; Hypothalamic and Visual Pathway Glioma; Intraocular Melanoma; Islet Cell Carcinoma (Endocrine Pancreas); Kaposi's Sarcoma; Kidney (Renal Cell) Cancer; Kidney Cancer; Laryngeal Cancer; Laryngeal Cancer; Leukemia, Acute Lymphoblastic; Leukemia, Acute Lymphoblastic; Leukemia, Acute Myeloid; Leukemia, Acute Myeloid; Leukemia, Chronic Lymphocytic; Leukemia; Chronic Myelogenous; Leukemia, Hairy Cell; Lip and Oral Cavity Cancer; Liver Cancer, Adult (Primary); Liver Cancer, Childhood (Primary); Lung Cancer, Non-Small Cell; Lung Cancer, Small Cell; Lymphoma, AIDS-Related; Lymphoma, Burkitt's; Lymphoma, Cutaneous T-Cell, see Mycosis Fungoides and Sezary Syndrome; Lymphoma, Hodgkin's; Lymphoma, Hodgkin's; Lymphoma, Hodgkin's During Pregnancy; Lymphoma, Non-Hodgkin's; Lymphoma, Non-Hodgkin's; Lymphoma, Non-Hodgkin's During Pregnancy; Lymphoma, Primary Central Nervous System; Macroglobulinemia, Waldenstrom's; Malignant Fibrous Histiocytoma of Bone/Osteosarcoma; Medulloblastoma; Melanoma; Melanoma, Intraocular (Eye); Merkel Cell Carcinoma; Mesothelioma, Adult Malignant; Mesothelioma; Metastatic Squamous Neck Cancer with Occult Primary; Multiple Endocrine Neoplasia Syndrome; Multiple Myeloma/Plasma Cell Neoplasm' Mycosis Fungoides; Myelodysplastic Syndromes; Myelodysplastic/Myeloproliferative Diseases; Myelogenous Leukemia, Chronic; Myeloid Leukemia, Adult Acute; Myeloid Leukemia, Childhood Acute; Myeloma, Multiple; Myeloproliferative Disorders, Chronic; Nasal Cavity and Paranasal Sinus Cancer; Nasopharyngeal Cancer; Nasopharyngeal Cancer; Neuroblastoma; Non-Hodgkin's Lymphoma; Non-Hodgkin's Lymphoma; Non-Hodgkin's Lymphoma During Pregnancy; Non-Small Cell Lung Cancer; Oral Cancer; Oral Cavity Cancer, Lip and; Oropharyngeal Cancer; Osteosarcoma/Malignant Fibrous Histiocytoma of Bone; Ovarian Cancer; Ovarian Epithelial Cancer; Ovarian Germ Cell Tumor; Ovarian Low Malignant Potential Tumor; Pancreatic Cancer; Islet Cell; Paranasal Sinus and Nasal Cavity Cancer; Parathyroid Cancer; Penile Cancer; Pheochromocytoma; Pineoblastoma and Supratentorial Primitive Neuroectodermal Tumors; Pituitary Tumor; Plasma Cell Neoplasm/Multiple Myeloma; Pleuropulmonary Blastoma; Pregnancy and Breast Cancer; Pregnancy and Hodgkin's Lymphoma; Pregnancy and Non-Hodgkin's Lymphoma; Primary Central Nervous System Lymphoma; Prostate Cancer; Rectal Cancer; Renal Cell (Kidney) Cancer; Renal Cell (Kidney) Cancer; Renal Pelvis and Ureter, Transitional Cell Cancer; Retinoblastoma; Rhabdomyosarcoma; Salivary Gland Cancer; Salivary Gland Cancer; Sarcoma, Ewing's Family of Tumors; Sarcoma, Kaposi's; Sarcoma, Soft Tissue; Sarcoma, Soft Tissue; Sarcoma, Uterine; Sezary Syndrome; Skin Cancer (non-Melanoma); Skin Cancer; Skin Cancer (Melanoma); Skin Carcinoma, Merkel Cell; Small Cell Lung Cancer; Small Intestine Cancer; Soft Tissue Sarcoma; Soft Tissue Sarcoma; Squamous Cell Carcinoma, see Skin Cancer (non-Melanoma); Squamous Neck Cancer with Occult Primary, Metastatic; Stomach (Gastric) Cancer; Stomach (Gastric) Cancer; Supratentorial Primitive Neuroectodermal Tumors; T-Cell Lymphoma, Cutaneous, see Mycosis Fungoides and Sezary Syndrome; Testicular Cancer; Thymoma; Thymoma and Thymic Carcinoma; Thyroid Cancer; Thyroid Cancer; Transitional Cell Cancer of the Renal Pelvis and Ureter; Trophoblastic Tumor, Gestational; Unknown Primary Site, Carcinoma of; Unknown Primary Site, Cancer of; Unusual Cancers of Childhood; Ureter and Renal Pelvis, Transitional Cell Cancer; Urethral Cancer; Uterine Cancer, Endometrial; Uterine Sarcoma; Vaginal Cancer; Visual Pathway and Hypothalamic Glioma; Vulvar Cancer; Waldenstrom's Macroglobulinemia; Wilms' Tumor; and Women's Cancers.
Neurologic diseases that may be treated include epilepsy, schizophrenia, bipolar disorder or other psychological and/or psychiatric disorders, neuropathies, skeletal muscle atrophy, and neurodegenerative diseases, e.g., a neurodegenerative disease. Exemplary neurodegenerative diseases include. Alzheimer's disease, Amyotrophic Lateral Sclerosis (ALS), and Parkinson's disease. Another class of neurodegenerative diseases includes diseases caused at least in part by aggregation of poly-glutamine. Diseases of this class include: Huntington's Diseases, Spinalbulbar Muscular Atrophy (SBMA or Kennedy's Disease), Dentatorubropallidoluysian Atrophy (DRPLA), Spinocerebellar Ataxia 1 (SCAT), Spinocerebellar Ataxia 2 (SCA2), Machado-Joseph Disease (MJD; SCA3), Spinocerebellar Ataxia 6 (SCA6), Spinocerebellar Ataxia 7 (SCAT), and Spinocerebellar Ataxia 12 (SCA12).
Any other disease in which the Wnt pathway, TGFβ pathway, JAK/STAT pathway, the mTOR pathway, Pgp modulation, CK1, CK1γ, CK2, or PIMs plays a role may be treatable or preventable using compounds and methods described herein.
Dosage
As used herein, a “therapeutically effective amount” or “therapeutically effective dose” is an amount of a compound of the invention or a combination of two or more such compounds, which inhibits, totally or partially, the progression of the condition or alleviates, at least partially, one or more symptoms of the condition. A therapeutically effective amount can also be an amount which is prophylactically effective. The amount which is therapeutically effective will depend upon the patient's size and gender, the condition to be treated, the severity of the condition and the result sought. For a given patient, a therapeutically effective amount may be determined by methods known to those of skill in the art.
A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms in a patient. Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the maximum tolerated dose (MTD) and the ED50 (effective dose for 50% maximal response). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between MTD and ED50. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. In the treatment of crises, the administration of an acute bolus or an infusion approaching the MTD may be required to obtain a rapid response.
Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the CK1, CK1γ, CK2, Piml-3, Wnt pathway, TGFβ pathway, JAK/STAT pathway, mTOR pathway, or Pgp modulating effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. HPLC assays or bioassays can be used to determine plasma concentrations.
Dosage intervals can also be determined using the MEC value. Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90% until the desired amelioration of symptoms is achieved. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.
The amount of composition administered will, of course, be dependent on the subject being treated, on the subject's weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.
Kits
The compounds and compositions of the invention (e.g., compounds and compositions of formula I) may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. Compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labelled for treatment of an indicated condition. Instructions for use may also be provided.
The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention. The geometric isomers depicted below are believed to be correct, but final structural assignment will be made via 2-D NMR experiments. Although the exemplary compounds described below are believed to be the Z-geometric isomers, the E-geometric isomers and mixtures of the E- and Z-isomers are also contemplated by the present disclosure.
(E)-4-(dimethylamino)-1,1-dimethoxybut-3-en-2-one (1): 1,1-dimethoxy-N,N-dimethylmethanamine (100 g, 839 mmol, 1.02 equiv.) and 1,1-dimethoxypropan-2-one (97 g, 821 mmol) were added and stirred at 110° C. for 3 hours. The produced methanol was removed by a Dean-Stark apparatus. After the solution was cooled to room temperature, the remaining volatile materials were removed in vacuo to provide 130 g of the crude product, (E)-4-(dimethylamino)-1,1-dimethoxybut-3-en-2-one (1) (130 g, 143 g theoretical, 91%). LC-MS m/z 283 (M+1). Reference: WO 2006/0097341A1, pg 67.
Sodium 4-(dimethoxymethyl)pyrimidine-2-thiolate (2): A solution of thiourea (64.7 g, 850 mmol, 1.13 equiv.), sodium methanolate (95%, 40.5 g, 751 mmol, 1.0 equiv.) in methanol (500 mL, 1.5 M) was stirred at room temperature for 30 minutes. A solution of (E)-4-(dimethylamino)-1,1-dimethoxybut-3-en-2-one (1) (130 g, 751 mmol) in methanol (200 mL) was added and the reaction stirred at room temperature for 2 h. The crude sodium 4-(dimethoxymethyl)pyrimidine-2-thiolate (2) was used directly in the next step without further purification. LC-MS m/z 209 (M+1). Reference: WO 2006/0097341A1, pg 67.
4-(dimethoxymethyl)-2-(methylthio)pyrimidine (3): Iodomethane (128 g, 902 mmol, 1.20 equiv.) was added carefully to the crude solution of sodium 4-(dimethoxymethyl)pyrimidine-2-thiolate (2) (156 g, 751 mmol) in methanol (700 mL, 1.1 M) while maintaining the reaction temperature below 28° C. using an ice-water bath for cooling. The resulting mixture was stirred at room temperature for 16 h. After removal of the solvent under reduced pressure, the residue was diluted with water (300 mL) and extracted with ethyl acetate (2×150 mL). The combined organic layer was concentrated under reduced pressure and the crude residue purified by passing through a short silica gel pad and washing with diethyl ether (200 mL) to afford 4-(dimethoxymethyl)-2-(methylthio)pyrimidine (3) as a brown oil (53.7 g, 150 g theoretical, 35.7%). LC-MS m/z 201 (M+1). Reference: WO 2006/0097341A1, pg 67.
2-(methylthio)pyrimidine-4-carbaldehyde (4): 4-(dimethoxymethyl)-2-(methylthio)pyrimidine (3) (53.7 g, 268 mmol) was added carefully to 1.2 N aqueous HCl (300 mL, 268 mmol, 1.0 equiv.) and stirred at 60° C. for 3 hours. The reaction mixture was then cooled to room temperature and neutralized by the slow addition of solid sodium bicarbonate. The crude mixture was extracted with diethyl ether (3×150 mL) and the combined organic layer was concentrated under reduced pressure to afford 2-(methylthio)pyrimidine-4-carbaldehyde (4) as a yellow solid (14.2 g, 41.5 g theoretical, 34%). LC-MS m/z 155 (M+1). Reference: WO 2006/009734 A1, pg 67.
(Z)-5-((2-(methylthio)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (5): A 40 mL round-bottomed vial was charged with 2-(methylthio)pyrimidine-4-carbaldehyde (4) (771 mg, 5 mmol), thiazolidine-2,4-dione (586 mg, 5 mmol, 1.0 equiv.), and piperidine (400 μL, 4 mmol, 0.8 equiv.) in ethanol (20 mL, 0.25 M). The reaction mixture was heated to 80° C. and shaken for 20 h. The resulting yellow precipitate was isolated by filtration and washed with ethanol (1×20 mL) and dried in vacuo to afford (Z)-5-((2-(methylthio)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (5) as a yellow solid (550 mg, 898 mg theoretical, 61%). LC-MS m/z 254 (M+1).
(Z)-5-((2-(methylsulfonyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (6): A mixture of (Z)-5-((2-(methylthio)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (5) (3.5 g, 13.82 mmol) in THF (100 mL, 0.13 M) was treated with a solution of oxone (25.8 g, 41.5 mmol, 3.0 equiv.) in water (175 mL). The resulting mixture was stirred at room temperature for 48 h. The resulting precipitate was filtered and washed with water (20 mL) and diethyl ether (20 mL) to afford (Z)-5-((2-(methylsulfonyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (6) as a solid (2.48 g, 3.94 g theoretical, 63%). LC-MS m/z 286 (M+1).
General Displacement Procedure 1: 2 dram round bottomed vials were charged with (Z)-5-((2-(methylsulfonyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (6) (25 mg, 0.0877 mmol), DMSO (1 mL, 0.08 M), diisopropylethylamine (50 μL, 0.288 mmol, 3.2 equiv.), and the appropriate amine (0.0877 mmol, 1.0 equiv.). The reaction mixture was heated to 120° C. and shaken for 16 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4).
(Z)-5-((2-(4-(benzo[d][1,3]dioxol-5-ylmethyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(benzo[d][1,3]dioxol-5-ylmethyl)piperazine (16.6 mg, 37.4 mg theoretical, 44.3%). LC-MS m/z 426.5 (M+1).
(Z)-5-((2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(p-tolyl)piperazine (12.5 mg, 33.6 mg theoretical, 37.2%). LC-MS m/z 382.5 (M+1).
(Z)-5-β2-(methyl(2-(pyridin-2-yl)ethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methyl-2-(pyridin-2-yl)ethanamine (13.7 mg, 30 mg theoretical, 45.6%). LC-MS m/z 342.4 (M+1).
(Z)-5-((2-(4-isopropylpiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-isopropylpiperazine (15.3 mg, 29.3 mg theoretical, 52.1%). LC-MS m/z 334.4 (M+1).
(Z)-5-((2-(3,4-dihydroisoquinolin-2(1H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,2,3,4-tetrahydroisoquinoline (0.1 mg, 29.8 mg theoretical, 0.3%). LC-MS m/z 339.4 (M+1).
(Z)-5-((2-(4-(pyridin-2-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(pyridin-2-yl)piperazine (25.7 mg, 32.4 mg theoretical, 79.3%). LC-MS m/z 369.4 (M+1).
(Z)-methyl 1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)pyrrolidine-2-carboxylate was prepared using the general displacement procedure and methylpyrrolidine-2-carboxylate (3.1 mg, 29.4 mg theoretical, 10.5%). LC-MS m/z 335.4 (M+1).
(Z)-5-β2-(4-methylpiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-methylpiperazine (0.1 mg, 26.9 mg theoretical, 0.4%). LC-MS m/z 306.4 (M+1).
(Z)-5-((2-(4-morpholinopiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 4-(piperidin-4-yl)morpholine (14.7 mg, 33 mg theoretical, 44.5%). LC-MS m/z 376.4 (M+1).
(Z)-tert-butyl (1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)pyrrolidin-3-yl)carbamate was prepared using the general displacement procedure and tert-butyl pyrrolidin-3-ylcarbamate (0.1 mg, 34.4 mg theoretical, 0.3%). LC-MS m/z 392.4 (M+1).
(Z)-5-((2-(4-(pyrimidin-2-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(piperazin-1-yl)pyrimidine (3.1 mg, 32.5 mg theoretical, 9.5%). LC-MS m/z 370.4 (M+1).
(Z)-5-((2-morpholinopyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and morpholine (7.8 mg, 25.7 mg theoretical, 30.3%). LC-MS m/z 293.3 (M+1).
(Z)-5-((2-(piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and piperidine (8.9 mg, 25.5 mg theoretical, 34.8%). LC-MS m/z 291.3 (M+1).
(Z)-5-((2-(pyrrolidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and pyrrolidine (8.3 mg, 24.3 mg theoretical, 34.1%). LC-MS m/z 277.3 (M+1).
(Z)-5-((2-(4-(pyrrolidin-1-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 4-(pyrrolidin-1-yl)piperidine (9.3 mg, 31.6 mg theoretical, 29.4%). LC-MS m/z 360.4 (M+1).
(Z)-tert-butyl 4-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperazine-1-carboxylate was prepared using the general displacement procedure and tert-butyl piperazine-1-carboxylate (6.7 mg, 34.4 mg theoretical, 19.5%). LC-MS m/z 392.4 (M+1).
(Z)-tert-butyl 4-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)-1,4-diazepane-1-carboxylate was prepared using the general displacement procedure and tert-butyl 1,4-diazepane-1-carboxylate (5.1 mg, 35.7 mg theoretical, 14.3%). LC-MS m/z 406.5 (M+1).
(Z)-5-((2-(4-(2-morpholino-2-oxoethyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-morpholino-2-(piperazin-1-yl)ethanone (11.4 mg, 36.8 mg theoretical, 31%). LC-MS m/z 419.5 (M+1).
(Z)-5-((2-(4-phenylpiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-phenylpiperazine (11.3 mg, 32.3 mg theoretical, 35%). LC-MS m/z 368.4 (M+1).
(Z)-5-((2-(methyl(phenethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methyl-2-phenylethanamine (8.3 mg, 30 mg theoretical, 27.7%). LC-MS m/z 341.4 (M+1).
(Z)-5-((2-(4-(pyridin-4-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(pyridin-4-yl)piperazine (7 mg, 32.4 mg theoretical, 21.6%). LC-MS m/z 369.4 (M+1).
(Z)-tert-butyl (1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)carbamate was prepared using the general displacement procedure and tert-butyl piperidin-4-ylcarbamate (5.9 mg, 35.7 mg theoretical, 16.5%). LC-MS m/z 406.5 (M+1).
(Z)-tert-butyl ((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-3-yl)methyl)carbamate was prepared using the general displacement procedure and tert-butyl (piperidin-3-ylmethyl)carbamate (0.1 mg, 36.9 mg theoretical, 0.3%). LC-MS m/z 420.5 (M+1).
(Z)-5-((2-(4-aminopiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl piperidin-4-ylcarbamate. The purified boc-protected was then treated with dichloromethane (1.0 mL), hydrochloric acid in methanol (500 μL, 1.25 M)) and shaken at 50° C. for 16 h. The reaction mixture was then concentrated under reduced pressure (Genevac HT-4) to provide (1.7 mg, 26.9 mg theoretical, 6.3%). LC-MS m/z 306.4 (M+1).
General displacement procedure 2: 2 dram round-bottomed vials were charged with (Z)-5-((2-(methylsulfonyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (25 mg, 0.0877 mmol), DMSO (1 mL, 0.08 M), diisopropylethylamine (50 μL, 0.288 mmol, 3.2 equiv.), and the appropriate amine (0.0877 mmol, 1.0 equiv.). The reaction mixture was heated to 110° C. and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4).
(Z)-5-((2-(4-benzoylpiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and phenyl(piperazin-1-yl)methanone (4.1 mg, 34.7 mg theoretical, 11.8%). LC-MS m/z 396 (M+1).
(R,Z)-5-((2-(4-benzyl-3-(hydroxymethyl)-5-oxopiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (R)-1-benzyl-6-(hydroxymethyl)piperazin-2-one (5.1 mg, 37.4 mg theoretical, 13.6%). LC-MS m/z 426 (M+1).
(Z)-N-(1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)pyrrolidin-3-yl)-N-ethylacetamide was prepared using the general displacement procedure and N-ethyl-N-(pyrrolidin-3-yl)acetamide (12.1 mg, 31.8 mg theoretical, 38%). LC-MS m/z 362 (M+1).
(Z)-5-((2-(3-(dimethylamino)pyrrolidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N,N-dimethylpyrrolidin-3-amine (12.2 mg, 28.1 mg theoretical, 43.4%). LC-MS m/z 320 (M+1).
(Z)-5-((2-(methyl(1-methylpyrrolidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N,1-dimethylpyrrolidin-3-amine (1.1 mg, 28.1 mg theoretical, 3.9%). LC-MS m/z 320 (M+1).
(Z)-5-((2-(4-(2-hydroxyethyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(piperazin-1-yl)ethanol (4.4 mg, 29.5 mg theoretical, 14.9%). LC-MS m/z 336 (M+1).
(Z)-5-((2-(4-(4-(trifluoromethyl)pyrimidin-2-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(piperazin-1-yl)-4-(trifluoromethyl)pyrimidine (5.8 mg, 38.5 mg theoretical, 15.1%). LC-MS m/z 438 (M+1).
(Z)-5-((2-(4-(4-(benzyloxy)phenyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(4-(benzyloxy)phenyl)piperazine (4 mg, 41.7 mg theoretical, 9.6%). LC-MS m/z 474 (M+1).
(Z)-5-((2-(4-(4-chloro-2-fluorophenyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(4-chloro-2-fluorophenyl)piperazine (4.8 mg, 36.9 mg theoretical, 13%). LC-MS m/z 420 (M+1).
(Z)-5-((2-(4-(4-(tert-butyl)phenyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(4-(tert-butyl)phenyl)piperazine (3.7 mg, 37.2 mg theoretical, 10%). LC-MS m/z 424 (M+1).
(Z)-5-((2-(4-(3,5-bis(trifluoromethyl)phenyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(3,5-bis(trifluoromethyl)phenyl)piperazine (3.8 mg, 44.3 mg theoretical, 8.6%). LC-MS m/z 504 (M+1).
(Z)-5-((2-(4-(4-(trifluoromethyl)pyrimidin-2-yl)-1,4-diazepan-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(4-(trifluoromethyl)pyrimidin-2-yl)-1,4-diazepane (4.9 mg, 39.7 mg theoretical, 12.3%). LC-MS m/z 452 (M+1).
(Z)-5-((2-(4-([1,1′-biphenyl]-4-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-([1,1′-biphenyl]-4-yl)piperazine (1.2 mg, 39 mg theoretical, 3.1%). LC-MS m/z 444 (M+1).
(Z)-5-((2-(4-(furan-2-carbonyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and furan-2-yl(piperazin-1-yl)methanone (6 mg, 33.9 mg theoretical, 17.7%). LC-MS m/z 386 (M+1).
(Z)-5-((2-(4-((4-fluorophenyl)(phenyl)methyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-((4-fluorophenyl)(phenyl)methyl)piperazine (14.4 mg, 41.8 mg theoretical, 34.4%). LC-MS m/z 476 (M+1).
(Z)-5-((2-(4-(naphthalen-1-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(naphthalen-1-yl)piperazine (6.2 mg, 36.7 mg theoretical, 16.9%). LC-MS m/z 418 (M+1).
(Z)-5-((2-(4-([1,1′-biphenyl]-3-yl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-([1,1′-biphenyl]-3-yl)piperazine (10.4 mg, 39 mg theoretical, 26.7%). LC-MS m/z 444 (M+1).
(Z)-5-((2-(4-((4-fluorophenyl)sulfonyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-((4-fluorophenyl)sulfonyl)piperazine (5.2 mg, 39.6 mg theoretical, 13.1%). LC-MS m/z 450 (M+1).
(Z)-1-tert-butyl 2-methyl 4-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperazine-1,2-dicarboxylate was prepared using the general displacement procedure and 1-tert-butyl 2-methyl piperazine-1,2-dicarboxylate (2.8 mg, 39.6 mg theoretical, 7%). LC-MS m/z 450 (M+1).
(Z)-5-((2-(4-benzyl-3-(hydroxymethyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (1-benzylpiperazin-2-yl)methanol (1.7 mg, 36.2 mg theoretical, 4.7%). LC-MS m/z 413 (M+1).
(Z)-5-((2-(5-oxo-1,4-diazepan-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,4-diazepan-5-one (1.1 mg, 28.1 mg theoretical, 3.9%). LC-MS m/z 320 (M+1).
(Z)-5-((2-(4-(4-(trifluoromethyl)phenyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(4-(trifluoromethyl)phenyl)piperazine (3.3 mg, 38.3 mg theoretical, 8.6%). LC-MS m/z 436 (M+1).
(Z)-5-((2-(4-cyclohexylpiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-cyclohexylpiperazine (10.7 mg, 32.9 mg theoretical, 32.5%). LC-MS m/z 374 (M+1).
(Z)-5-((2-(methyl(3-(piperidin-1-yl)propyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methyl-3-(piperidin-1-yl)propan-1-amine (10.2 mg, 31.8 mg theoretical, 32.1%). LC-MS m/z 362 (M+1).
(Z)-5-((2-(4-((1-methylpiperidin-4-yl)methyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-((1-methylpiperidin-4-yl)methyl)piperazine (7.3 mg, 42.3 mg theoretical, 17.2%). LC-MS m/z 403 (M+1).
(Z)-1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)-N-(2-hydroxyethyl)piperidine-4-carboxamide was prepared using the general displacement procedure and N-(2-hydroxyethyl)piperidine-4-carboxamide (10.8 mg, 39.7 mg theoretical, 27.2%). LC-MS m/z 378 (M+1).
(Z)-5-((2-(4-(4-methylpiperazine-1-carbonyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (4-methylpiperazin-1-yl)(piperidin-4-yl)methanone (5.5 mg, 43.8 mg theoretical, 12.6%). LC-MS m/z 417 (M+1).
(Z)-5-((2-(4-(4-methylpiperazin-1-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-methyl-4-(piperidin-4-yl)piperazine (12.4 mg, 40.9 mg theoretical, 30.4%). LC-MS m/z 389 (M+1).
(Z)-5-((2-(4-(dimethylamino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N,N-dimethylpiperidin-4-amine (5 mg, 35.1 mg theoretical, 14.3%). LC-MS m/z 334 (M+1).
(Z)-1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidine-4-carbonitrile was prepared using the general displacement procedure and piperidine-4-carbonitrile (7.5 mg, 33.2 mg theoretical, 22.6%). LC-MS m/z 316 (M+1).
(Z)-5-((2-((2-hydroxy-2-phenylethyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(methylamino)-1-phenylethanol (10.8 mg, 37.5 mg theoretical, 28.8%). LC-MS m/z 357 (M+1).
General displacement procedure 3: 2 dram round-bottomed vials were charged with (Z)-5-((2-(methylsulfonyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (50 mg, 0.175 mmol), DMSO (2 mL, 0.08 M), diisopropylethylamine (34 μL, 0.193 mmol, 1.1 equiv.), and the appropriate amine (0.175 mmol, 1.0 equiv.). The reaction mixture was heated to 100° C. and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4). The crude was then charged with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4).
(Z)-5-((2-(4-(aminomethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl (piperidin-4-ylmethyl)carbamate (49 mg, 55.9 mg theoretical, 88%). LC-MS m/z 320 (M+1).
(Z)-5-((2-(methyl(piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 3-(methylamino)piperidine-1-carboxylate (2.3 mg, 55.9 mg theoretical, 4.1%). LC-MS m/z 320 (M+1).
(Z)-5-((2-(3-methylpiperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 2-methylpiperazine-1-carboxylate (1.5 mg, 53.4 mg theoretical, 2.8%). LC-MS m/z 306 (M+1).
(Z)-5-((2-(piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl piperazine-1-carboxylate (17.7 mg, 51 mg theoretical, 34.7%). LC-MS m/z 292 (M+1).
(Z)-5-((2-(1,4-diazepan-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 1,4-diazepane-1-carboxylate (15.2 mg, 53.4 mg theoretical, 28.4%). LC-MS m/z 306 (M+1).
(Z)-5-((2-(3-aminopyrrolidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl pyrrolidin-3-ylcarbamate (16.5 mg, 51 mg theoretical, 32.4%). LC-MS m/z 292 (M+1).
(Z)-5-((2-(3-aminopiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl piperidin-3-ylcarbamate (16.9 mg, 29.8 mg theoretical, 53.4%). LC-MS m/z 306 (M+1).
A 25 mL round-bottomed flask was charged with 2-methoxyethanol (57 μL, 1 equiv.) and THF (2.5 mL). 60% NaH in oil (21 mg, 1.1 equiv.) was added at 0° C. under argon. The reaction mixture was stirred for 5 min at −5° C. and for 1 h 15 min at RT. Methyl 2,6-dichloropyrimidine-4-carboxylate (150 mg, 1 equiv.) dissolved in THF (1 mL) was added over 5 min at −78° C. The reaction mixture was stirred for 4 h warming from −78° C. to 0° C. LC-MS after 3 h (−15° C.) showed 2 peaks (2:1 ratio) with the desired mass at 1.57 min and 1.67 min (M+1=247 & 249). The reaction mixture was quenched with 10% NH4Cl (5 mL) at 0° C. The aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide 161 mg of a crude mixture of methyl 2-chloro-6-(2-methoxyethoxy)pyrimidine-4-carboxylate and methyl 6-chloro-2-(2-methoxyethoxy)pyrimidine-4-carboxylate which was partially separated by flash chromatography on silica gel (10 g, Hexanes/EtOAc 9:1 to 7:3).
A 25 mL round bottomed flask was charged with methyl 2-chloro-6-(2-methoxyethoxy)pyrimidine-4-carboxylate [SAD105-047F1] (45 mg, 1 equiv.) and CH2Cl2 (1 mL). 1 M DIBAL-H (0.2 mL, 1.1 equiv.) was added at −78° C. over 2 min under argon. The reaction mixture was stirred for 3 h at −78° C. but the LC-MS still showed a lot of starting material. Additional 1 M DIBAL-H (0.27 mL, 1.4 equiv.) was added at −78° C. over 2 min under argon and after 0.5 h LC-MS showed no more starting material but mostly 1 peak at 1.20 min (M+1=217, M+l+MeOH=249). The reaction mixture was quenched with MeOH (0.5 mL) and then with 10% NH4Cl (1 mL). The reaction mixture was warmed to RT and then the solvent was concentrated under reduced pressure. The residue was diluted with 10% NH4Cl (4 mL). The aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide 41.9 mg of the crude 2-chloro-6-(2-methoxyethoxy)pyrimidine-4-carbaldehyde as a yellow oil which was used in the next step without further purification, (H NMR δ: 9.91 (s, 1H); 7.23 (s, 1H); 4.59-4.64 (m, 2H), 3.7-3.8 (m, 2H); 3.44 (s, 3H).
Crude 2-chloro-6-(2-methoxyethoxy)pyrimidine-4-carbaldehyde (sad105-052, 41.9 mg) was dissolved in ethanol (1.5 mL) and was added to a 10 mL vial containing the thiazolidine-dione (21.3 mg, 0.18 mmol) and the 1-(p-tolyl)piperazine (39.3 mg, 0.18 mmol). The reaction mixture was shaken at 80° C. for 15.5 h. LC-MS showed a peak with the desired mass at 2.18 min (M+1=456). The solvent was concentrated under reduced pressure and the residue was dissolved in EtOAc (20 mL) and washed with saturated NaHCO3 (10 mL). The organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide 85.7 mg of brown oil. Purification by flash chromatography (SiO2,10 g, Hexanes/EtOAc 9:1 to 6:4 to 1:1) provided 11.5 mg (13.9% 2 steps, 83 mg theoretical) of pure (Z)-5-((6-(2-methoxyethoxy)-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione as a yellow solid.
A 40 mL round-bottomed vial was charged with methanol (120 μL of 200 μL MeOH in 1 mL Acetonitrile, 1 equiv.), K2CO3 (67 mg, 1 equiv.), methyl 2,6-dichloropyrimidine-4-carboxylate (100 mg, 1 equiv.), and acetonitrile (2 mL). The reaction mixture was shaken for 2.5 h at RT but LC-MS showed only starting material. The reaction mixture was then shaken for 1 h at 85° C. LC-MS showed the formation of a small amount of desired product (1.51 min, M+1=203). Methanol (0.200 mL, 10 equiv.) was added and the reaction mixture was shaken for 15 h at 85° C. LC-MS showed mostly 1 peak in the UV and MS at 1.53 min and a tiny amount of bis-methoxypyrimidine. The solid precipitate was filtered off and the filtrate was evaporated to give 89 mg (91% crude yield, theoretical 98 mg) of crude desired product. 1H NMR showed an 11:1 mixture of desired product and bis-methoxypyrimidine side product (M+1=199). The material was used in the next step without further purification.
A 25 mL round-bottomed flask was charged with methyl 2-chloro-6-methoxypyrimidine-4-carboxylate [sad105-055 crude] (74 mg, 1 equiv.) under argon. 1M DIBAL-H in dichloromethane (0.73 mL, 2 equiv.) was added over 5 min and the reaction mixture was stirred at −78° C. for 45 min. After 0.5 h, LC-MS showed the reaction was complete. The reaction was quenched at −78° C. with methanol (0.5 mL) and then with 10% NH4Cl (2 mL). The solvents were concentrated under reduced pressure and the residue was diluted with 10% NH4Cl (3 mL). The aqueous layer was extracted with EtOAc (3×10 mL). The combined organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide the crude product 2-chloro-6-methoxypyrimidine-4-carbaldehyde as an orange oil (76 mg, 63 mg theoretical, 121%). LC-MS m/z: 205.0: (M+1+MeOH, hemiacetal with methanol). Some over-reduced alcohol was also observed in the crude (2.17 min, M+1=175). The crude aldehyde was used directly in the next step without further purification.
Crude 2-chloro-6-methoxypyrimidine-4-carbaldehyde (sad105-058, 76 mg) was dissolved in ethanol (2 mL) and was added to a 10 mL vial containing the thiazolidine-dione (42.8 mg, 0.37 mmol., 1 equiv.) and the 1-(p-tolyl)piperazine (70.8 mg, 0.40 mmol, 1.1 equiv.). The mixture was shaken for 45 h at 80° C. and for 15 h at 90° C. producing a precipitate. LC-MS of the solution showed some product at (M+1=412) and some intermediate at (M+1=430). The desired product crashed out of the solution and the LC-MS of the solution does not reflect well the conversion of the reaction. The yellow solid was filtered using a Pasteur pipette through a pad of glass wool and the solid was rinsed with EtOH (4×0.5 mL). The ethanol filtrate contains some desired product. The solid was re-dissolved in CH2Cl2 and the insoluble solid was filtered off. The filtrate was concentrated under reduced pressure to provide 20 mg of the desired product (Z)-5-((6-methoxy-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (97.3% pure). The insoluble solid was partitioned between saturated NaHCO3 (3 mL) and CH2Cl2 (2×5 mL). The organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide an additional 13.4 mg of the desired product (total 33.4 mg, 150 mg theoretical, 22%). LC-MS m/z: 412 (M+1).
A 40 mL round-bottomed vial was charged with methyl 2-chloroisonicotinate (200 mg, 1.17 mmol, 1 equiv.) and 1-(p-tolyl)piperazine (205 mg, 1.17 mmol, 1 equiv.). Toluene (3 mL) and DMSO (3 mL) were added followed by potassium carbonate (403 mg, 2.9 mmol, 2.5 equiv.). The mixture was shaken for 18 h at 100° C. LC-MS after 18 h showed a peak at 1.68 min with the desired mass (M+1=312) with the chloropyridine starting material co-eluting (M+1=172). The reaction mixture was diluted with water (5 mL) and the aqueous layer was extracted with CH2Cl2 (3×10 mL). The combined organic layer was dried over Na2SO4 and then concentrated under reduced pressure. The crude mixture was purified on silica gel (10 g, Hexanes/EtOAc 9:1 to 1:1) to provide the desired product as white crystals (27 mg, 67 mg theoretical, 40%).
A 25 mL round-bottomed flask was charged with methyl 2-(4-(p-tolyl)piperazin-1-yl)isonicotinate (27 mg, 0.087 mmol, 1 equiv.) and CH2Cl2 (1 mL). 1 M DIBAL-H in CH2Cl2 (130 μL, 0.13 mmol, 1.5 equiv.) was added under argon at −78° C. over 2 min. The reaction mixture was quenched with MeOH (0.5 mL) at −78° C. The LC-MS of the crude mixture showed a 1:1 mixture of the alcohol (1.21 min, M+1=284) and the aldehyde as a hemiacetal with methanol (1.38 min, M+1+MeOH=314.3). The crude aldehyde was used directly in the next step without any further purification.
Crude 2-(4-(p-tolyl)piperazin-1-yl)isonicotinaldehyde [sad105-080] was dissolved in ethanol (1 mL) and was added to a 10 mL vial containing the thiazolidine-dione (10.2 mg, 0.087 mmol) and the 1-(p-tolyl)piperazine (5.9 mg, 0.087 mmol). The reaction mixture was shaken at 90° C. for 19.5 h. LC-MS showed a new peak with the desired mass at 1.78 min (M+1=381). The reaction was concentrated under reduced pressure and the residue was purified by flash chromatography (SiO2,10 g, Hexanes/EtOAc 9:1 to 4:6) to provide 10.1 mg (30% over two steps, 33.1 mg theoretical) of (Z)-5-(2-(4-(p-tolyl)piperazin-1-yl)pyridin-4-yl)methylene)thiazolidine-2,4-dione as a yellow solid. The yellow solid was dissolved in hot EtOH (0.5 mL). On cooling a yellow solid precipitated, which was filtered through a pad of glass wool and washed with 0.25 mL ethanol. The solid was re-dissolved in CH2Cl2 and was concentrated under reduced pressure to provide 1.7 mg of the title product. LC-MS m/z: (M+1=381).
A 40 mL round-bottomed vial was charged with thiazolidine-2,4-dione (300 mg, 2.56 mmol, 1 equiv.) and 6-bromopicolinaldehyde (477 mg, 2.56 mmol, 1 equiv.). Toluene (5 mL, 0.5 M), glacial acetic acid (22 μL, 0.38 mmol, 0.15 equiv.), and piperidine (25 μL, 0.25 mmol, 0.1 equiv.) were added and the vial was purged with argon. The mixture was shaken for 16 h at 125° C. The resulting solid was collected by filtration and then washed with acetone (3×5 mL). The solid was dried under reduced pressure to provide (Z)-5-((6-bromopyridin-2-yl)methylene)thiazolidine-2,4-dione (439 mg, 731 mg theoretical, 60%). LC-MS m/z: 286 (M+1).
An 8 mL round bottomed vial was charged with 1-(p-tolyl)piperazine (56 mg, 0.318 mmol, 1 equiv.) and DMSO (1 mL, 0.3 M), DiPEA (105 μL, 0.636 mmol, 2 equiv.), (Z)-5-((6-bromopyridin-2-yl)methylene)thiazolidine-2,4-dione (91 mg, 0.318 mmol, 1 equiv.), and the vial was purged with argon. The mixture was shaken for 48 h at 110° C. The reaction mixture was then partitioned between CH2Cl2 (10 mL) and sat. NaCl (20 mL). The aqueous layer was back extracted with CH2Cl2 (2×15 mL) and the combined organic layer was dried over xxx and concentrated under reduced pressure to provide an orange residue. The orange residue was triturated with ether (3×15 mL) to provide (Z)-5-((6-(4-(p-tolyl)piperazin-1-yl)pyridin-2-yl)methylene)thiazolidine-2,4-dione as an orange solid (65 mg, 122 mg theoretical, 53%). LC-MS m/z: 382 (M+1).
An 8 mL round-bottomed vial was charged with N-methyl-2-phenylethanamine (43 mg, 0.318 mmol, 1 equiv.) and DMSO (1 mL, 0.3 M), DiPEA (105 μL, 0.636 mmol, 2 equiv.), (Z)-5-((6-bromopyridin-2-yl)methylene)thiazolidine-2,4-dione (91 mg, 0.318 mmol, 1 equiv.), and the vial was purged with argon. The mixture was shaken for 48 h at 110° C. The reaction mixture was then partitioned between CH2Cl2 (10 mL) and sat. NaCl (20 mL). The aqueous layer was back extracted with CH2Cl2 (2×15 mL) and the combined organic layer was dried over xxx and concentrated under reduced pressure to provide an orange residue. The orange residue was triturated with ether (3×15 mL) to provide (Z)-5-((6-(methyl(phenethyl)amino)pyridin-2-yl)methylene)thiazolidine-2,4-dione as an orange film (2.6 mg, 175 mg theoretical, 5%). LC-MS m/z: 340 (M+1).
General Procedure 1 for the Preparation of Amino-Analogs
Methyl 2,6-dichloropyrimidine-4-carboxylate (200 mg, 0.966 mmol) in 2 mL of THF was treated with DIPEA (185 μL, 1.06 mmol) and the reaction was then cooled to 0° C. A solution of the appropriate amine (1 equiv., 0.966 mmol) in 2 mL of THF was then added slowly to the reaction mixture. The reaction mixture was shaken for 2 h and then concentrated under reduced pressure to provide a light yellow crude product, which was used without any further purification.
The light yellow crude product (1 equiv.) was treated with DCM (2 mL). The reaction mixture was then cooled to −70° C. and treated dropwise with 1 M DIBALH (180 μL, 1.1 equiv.) and stirred for 2 h. Another 100 μL of DIBALH was added dropwise and stirred for an additional 3 h. MeOH (1 mL) was then added to quench the reaction. The reaction mixture was then allowed to warm to room temperature and partitioned between water (5 mL) and DCM (5 mL). The DCM layer was collected and concentrated under reduced pressure. Flash chromatography using 50%-80% EtOAc/Hexanes provided the desired aldehyde.
The aldehyde was treated with thiazolidine-2,4-dione (1 equiv.) and 1-(p-tolyl)piperazine (1.1 equiv.) in 2 mL of EtOH. The reaction mixture was then heated to 85° C. for 16 h and then further heated to 95° C. for 24 h. The reaction mixture was then concentrated and purified by Biotage chromatography using 1:1 hexanes/EtOAc to provide the final amino-analogs.
(Z)-5-((6-(methyl(phenethyl)amino)-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using General Procedure 1 for the Preparation of Amino-Analogs and N-methyl-2-phenylethanamine (4.2 mg, 90 mg theoretical, 5%, 3 steps). LC-MS m/z: 515 (M+1).
(Z)-5-((6-(benzyl(methyl)amino)-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using General Procedure 1 for the Preparation of Amino-Analogs and N-methylbenzylamine (5.1 mg, 85 mg theoretical, 6%, 3 steps). LC-MS m/z: 501 (M+1).
(Z)-5-((6-((2-methoxyethyl)(methyl)amino)-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methyl-1-phenylmethanamine (34 mg, 142 mg theoretical, 23.9%, 3 steps). LC-MS m/z 501: (M+1).
General Procedure 2 for the Preparation of Amino-Analogs
Methyl 2,6-dichloropyrimidine-4-carboxylate (200 mg, 0.966 mmol) in 2 mL of THF was treated with DIPEA (185 μL, 1.06 mmol) and then cooled to 0° C. A solution of the appropriate amine (1 equiv., 0.966 mmol) in 2 mL of THF was then added slowly. The reaction mixture was shaken for 2 h and concentrated under reduced pressure to provide a light yellow crude product, which was used without any further purification.
The crude material was treated with 2 mL of EtOH, DIPEA (1.1 equiv.), and 1-(p-tolyl)piperazine (1 equiv.). The reaction mixture was then heated to 90° C. for 2 d. LCMS showed the desired product along with the EtO version of the ester. The reaction mixture was then concentrated under reduced pressure and purified using a Biotage with 10-100% EtOAc/Hexanes to provide the desired di-aminoester intermediate.
The di-aminoester intermediate was treated with DCM (2 mL) and cooled to −10° C. DIBALH (3 equiv.) was added dropwise and the reaction mixture was allowed to warm to room temperature and stirred for 1 h. Methanol (1 mL) was added to quench the reaction and then allowed to stir for 30 min. The reaction mixture was then partitioned between DCM (10 mL) and H2O (10 mL). The aqueous layer was back extracted with DCM (2×10 mL) and the combined organic layer was concentrated under reduced pressure. The crude residue was purified on silica gel using 5-10% MeOH/DCM to provide the desired alcohol.
The alcohol (1 equiv.) was treated with 2 mL of DCM and the reaction mixture was cooled to 0° C. and treated with 1.4 mL of 15% Dess Martin reagent in DCM. The reaction mixture was stirred for 1 h and treated with an additional portion of Dess Martin reagent (1.1 equiv.) at 0° C., and the reaction mixture was allowed to warm to room temperature and stirred for 1 h. The reaction mixture was then concentrated under reduced pressure and the crude residue was purified by flash chromatography using 5-10% MeOH/DCM to provide the desired aldehyde.
The aldehyde was treated with thiazolidine-2,4-dione (1 equiv.), piperidine (0.8 equiv.), and 2 mL of EtOH. The reaction mixture was then heated to 85° C. for 16 h and then concentrated under reduced pressure. The residue was then triturated with DCM (2 mL), MeOH (2 mL), and EtOAc (2 mL) to provide the final amino-analogs.
(Z)-5-((6-(methyl(2-(pyridin-2-yl)ethyl)amino)-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methyl-2-(pyridin-2-yl)ethanamine (12.7 mg, 160 mg theoretical, 1.7%, 5 steps). LC-MS m/z: 516 (M+1).
(Z)-5-((6-((2-methoxyethyl)(methyl)amino)-2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-methoxy-N-methylethanamine (34 mg, 680 mg theoretical, 5%, 5 steps). LC-MS m/z: 469 (M+1).
To 10 mg of (Z)-5-((2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was added 4 mg of 2-bromoacetamide, 4 mg of potassium carbonate, and 0.5 mL of DMF. The reaction mixture was heated to 55° C. for 4 h, concentrated under reduced pressure, and purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient using trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide (Z)-2-(2,4-dioxo-5-((2-(4-(p-tolyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidin-3-yl)acetamide (4 mg, 11.5 mg theoretical, 35%). LC-MS m/z: 439 (M+1).
General Displacement Procedure:2 dram round-bottomed vials were charged with (Z)-5-((2-(methylsulfonyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione (25 mg, 0.0877 mmol) prepared according to the general procedure, DMSO (1 mL, 0.08 M), diisopropylethylamine (50 μL, 0.288 mmol, 3.2 equiv.), and the appropriate amine (0.0877 mmol, 1.0 equiv.). The reaction mixture was heated to 110° C. and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4).
(Z)-5-((2-(4-(3-(pyridin-4-yl)-1,2,4-oxadiazol-5-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 5-(piperidin-4-yl)-3-(pyridin-4-yl)-1,2,4-oxadiazole (6 mg, 45.8 mg theoretical, 13%). LC-MS m/z 436.4 (M+1).
(Z)-5-((2-(butylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methylbutan-1-amine (12.5 mg, 30.7 mg theoretical, 40.7%). LC-MS m/z 293.3 (M+1).
(Z)-5-((2-(isoquinolin-2(1H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure 1,2,3,4-tetrahydroisoquinoline (2 mg, 35 mg theoretical, 5.7%). LC-MS m/z 337.1 (M+1).
(Z)-5-((2-(methyl(pyridin-4-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methylpyridin-4-amine (11.7 mg, 32.9 mg theoretical, 35.5%). LC-MS m/z 314.3 (M+1).
(Z)-5-((2-(7-amino-3,4-dihydroisoquinolin-2(1H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,2,3,4-tetrahydroisoquinolin-7-amine (12.8 mg, 37.2 mg theoretical, 34.4%). LC-MS m/z 354.3 (M+1).
(Z)-5-((2-(3,4-dihydro-1H-pyrido[4,3-b]indol-2(5H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indole (4.2 mg, 39.7 mg theoretical, 10.6%). LC-MS m/z 378.4 (M+1).
(Z)-5-((2-(((1-methylpiperidin-4-yl)methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(methylpiperidin-4-yl)methanamine (7.4 mg, 29.2 mg theoretical, 25.3%). LC-MS m/z 334.1 (M+1).
(Z)-5-((2-(4-(2-(dimethylamino)ethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N,N-dimethyl-2-(piperidin-4-yl)ethanamine (20.6 mg, 38.0 mg theoretical, 54.2%). LC-MS m/z 362.2 (M+1).
(Z)-5-((2-(4-(1H-indol-3-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-(piperidin-4-yl)-1H-indole (7.2 mg, 42.6 mg theoretical, 16.8%). LC-MS m/z 406.1 (M+1).
(Z)-5-((2-(4-(1H-indol-3-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N,N-dimethyl-1-(piperidin-4-yl)methanamine (23.1 mg, 36.5 mg theoretical, 63.2%). LC-MS m/z 348.1 (M+1).
(Z)-5-((2-(3-fluoropiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-fluoropiperidine (7.7 mg, 32.4 mg theoretical, 23.7%). LC-MS m/z 309.1 (M+1).
(Z)-5-((2-(4-methylpiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 4-methylpiperidine (16.4 mg, 32 mg theoretical, 51.2%). LC-MS m/z 305.1 (M+1).
(Z)-5-((2-(4-(hydroxymethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and piperidin-4-ylmethanol (17.8 mg, 33.7 mg theoretical, 52.8%). LC-MS m/z 321.1 (M+1).
(Z)-5-((2-(3,5-dimethylpiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3,5-dimethylpiperidine (1.3 mg, 33.5 mg theoretical, 3.9%). LC-MS m/z 319.1 (M+1).
(Z)-5-((2-(8-methyl-2,8-diazaspiro[5.5]undecan-2-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-methyl-2,8-diazaspiro[5.5]undecane (23.5 mg, 39.3 mg theoretical, 59.8%). LC-MS m/z 374.2 (M+1).
(Z)-5-((2-(3-(piperidin-1-ylmethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(piperidin-3-ylmethyl)piperidine (21.8 mg, 40.7 mg theoretical, 53.5%). LC-MS m/z 388.5 (M+1).
(Z)-5-((2-(2-(2-hydroxyethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(piperidin-2-yl)ethanol (10.1 mg, 35.2 mg theoretical, 28.7%). LC-MS m/z 335.1 (M+1).
(Z)-5-((2-(3-(1H-pyrazol-1-yl)azetidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(azetidin-3-yl)-1H-pyrazole (24.3 mg, 34.5 mg theoretical, 70.4%). LC-MS m/z 329.1 (M+1).
(Z)-5-((2-(3-((dimethylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N,N-dimethyl-1-(piperidin-3-yl)methanamine (23.4 mg, 36.5 mg theoretical, 64.1%). LC-MS m/z 348.4 (M+1).
(Z)-5-((2-(8-benzyl-2,8-diazaspiro[5.5]undecan-2-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-benzyl-2,8-diazaspiro[5.5]undecane (15.3 mg, 47.3 mg theoretical, 32.4%). LC-MS m/z 450.5 (M+1).
(Z)-5-((2-(4-(2-hydroxyethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(piperidin-4-yl)ethanol (18.1 mg, 47.2 mg theoretical, 38.4%). LC-MS m/z 335.1 (M+1).
(Z)-5-((2-(4-(2-(piperidin-1-yl)ethyl)piperazin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(2-(piperidin-1-yl)ethyl)piperazine (36.6 mg, 66.3 mg theoretical, 55.2%). LC-MS m/z 403.2 (M+1).
(Z)-5-((2-(2-methylpiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-methylpiperidine (2.5 mg, 32 mg theoretical, 7.8%). LC-MS m/z 305.1 (M+1).
(Z)-5-((2-(4-hydroxypiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and piperidin-4-ol (19.9 mg, 33.7 mg theoretical, 52.8%). LC-MS m/z 321.1 (M+1).
(Z)-5-((2-(4-fluoropiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 4-fluoropiperidine (12 mg, 32.4 mg theoretical, 37%). LC-MS m/z 309.1 (M+1).
(Z)-5-((2-(3-(pyrrolidin-1-ylmethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-(pyrrolidin-1-ylmethyl)piperidine (4.3 mg, 39.3 mg theoretical, 11%). LC-MS m/z 374.5 (M+1).
(Z)-5-((2-((2-(dimethylamino)ethyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N1,N1,N2-trimethylethane-1,2-diamine (5.6 mg, 32.3 mg theoretical, 17.3%). LC-MS m/z 308.4 (M+1).
(S,Z)-5-((2-((1-hydroxybutan-2-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and amine (6.6 mg, 30.9 mg theoretical, 21.3%). LC-MS m/z 295.1 (M+1).
(Z)-5-((2-(3-(hydroxymethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (S)-2-aminobutan-1-ol (13.5 mg, 33.7 mg theoretical, 40.1%). LC-MS m/z 321.1 (M+1).
(Z)-5-((2-(4,4-bis(hydroxymethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and piperidine-4,4-diyldimethanol (10 mg, 36.8 mg theoretical, 27.1%). LC-MS m/z 351.1 (M+1).
(Z)-5-((2-(3-hydroxypiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and piperidin-3-ol (6.3 mg, 32.2 mg theoretical, 19.6%). LC-MS m/z 307.1 (M+1).
(Z)-5-((2-(3-methylpiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-methylpiperidine (10.3 mg, 32 mg theoretical, 32.2%). LC-MS m/z 305.1 (M+1).
(S,Z)-5-((2-(methyl(1-methylpiperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (S)—N,1-dimethylpiperidin-3-amine (11.2 mg, 58.4 mg theoretical, 19.2%). LC-MS m/z 334.1 (M+1).
(Z)-5-((2-(cyclohexyl(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methylcyclohexanamine (3.4 mg, 33.5 mg theoretical, 10.2%). LC-MS m/z 319.1 (M+1).
(Z)-5-((2-(5-amino-3,4-dihydroisoquinolin-2(1H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,2,3,4-tetrahydroisoquinolin-5-amine (8.2 mg, 37.2 mg theoretical, 22%). LC-MS m/z 354.1 (M+1).
(Z)-5-((2-(cyclohexylamino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and cyclohexanamine (3.6 mg, 32 mg theoretical, 11.2%). LC-MS m/z 305.1 (M+1).
(Z)-1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidine-4-carboxamide was prepared using the general displacement procedure and piperidine-4-carboxamide (16.7 mg, 35.1 mg theoretical, 47.6%). LC-MS m/z 334.1 (M+1).
(Z)-5-((2-((4-(m-tolylamino)-5,6,7,8-tetrahydroquinazolin-6-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N4-(m-tolyl)-5,6,7,8-tetrahydroquinazoline-4,6-diamine (5.2 mg, 48.3 mg theoretical, 10.8%). LC-MS m/z 460.5 (M+1).
(Z)-5-((2-(4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-8-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-phenyl-1,3,8-triazaspiro[4.5]decan-4-one (12.4 mg, 38.2 mg theoretical, 32.4%). LC-MS m/z 437.1 (M+1).
(Z)-5-((2-(3-(3-ethyl-1,2,4-oxadiazol-5-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-ethyl-5-(piperidin-3-yl)-1,2,4-oxadiazole (11.9 mg, 33.9 mg theoretical, 35.1%). LC-MS m/z 387.1 (M+1).
(Z)-5-((2-(4-(4,6-diamino-1,3,5-triazin-2-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 6-(piperidin-4-yl)-1,3,5-triazine-2,4-diamine (13.0 mg, 35.0 mg theoretical, 37.1%). LC-MS m/z 400.1 (M+1).
(Z)-5-((2-(3-((1H-benzo[d]imidazol-2-yl)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(piperidin-3-ylmethyl)-1H-benzo[d]imidazole (29.3 mg, 44.2 mg theoretical, 66.3%). LC-MS m/z 421.5 (M+1).
(Z)-5-((2-(3-(4-methyl-1H-benzo[d]imidazol-2-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 4-methyl-2-(piperidin-3-yl)-1H-benzo[d]imidazole (18.9 mg, 44.2 mg theoretical, 42.7%). LC-MS m/z 421.5 (M+1).
(Z)-5-((2-(4-(6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepin-3-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-(piperidin-4-yl)-6,7,8,9-tetrahydro-5H-[1,2,4]triazolo[4,3-a]azepine (16.2 mg, 44.7 mg theoretical, 36.2%). LC-MS m/z 426.5 (M+1).
(Z)-5-((2-(((1-ethyl-1H-pyrazol-5-yl)methyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(1-ethyl-1H-pyrazol-5-yl)-N-methylmethanamine (7.2 mg, 36.2 mg theoretical, 20%). LC-MS m/z 345.1 (M+1).
(Z)-5-((2-(3-(6-hydroxy-2-methylpyrimidin-4-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-methyl-6-(piperidin-3-yl)pyrimidin-4-ol (16.8 mg, 41.9 mg theoretical, 40.1%). LC-MS m/z 399.1 (M+1).
(Z)-5-((2-(3-([1,2,4]triazolo[4,3-a]pyridin-3-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-(piperidin-3-yl)-[1,2,4]triazolo[4,3-a]pyridine (11 mg, 42.8 mg theoretical, 25.7%). LC-MS m/z 408.5 (M+1).
(Z)-5-((2-(4-amino-3,4-dihydroisoquinolin-2(1H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,2,3,4-tetrahydroisoquinolin-4-amine (1.4 mg, 37.2 mg theoretical, 3.8%). LC-MS m/z 354.1 (M+1).
(Z)-5-((2-(4-(1H-tetrazol-5-yl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 4-(1H-tetrazol-5-yl)piperidine (4 mg, 37.7 mg theoretical, 10.6%). LC-MS m/z 359.1 (M+1).
(Z)-5-((2-(methyl(thiophen-3-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and N-methyl-1-(thiophen-3-yl)methanamine (7.5 mg, 35 mg theoretical, 21.5%). LC-MS m/z 333.0 (M+1).
(Z)-5-((2-(2,4-dioxo-1,3,8-triazaspiro[4.5]decan-8-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,3,8-triazaspiro[4.5]decane-2,4-dione (15.2 mg, 39.4 mg theoretical, 38.6%). LC-MS m/z 375.1 (M+1).
(Z)-5-((2-(((1H-benzo[d]imidazol-2-yl)methyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1-(1H-benzo[d]imidazol-2-yl)-N-methylmethanamine (6.6 mg, 38.5 mg theoretical, 17%). LC-MS m/z 367.1 (M+1).
(Z)-5-((2-((3-aminobenzyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-((methylamino)methyl)aniline (19.7 mg, 35.9 mg theoretical, 54.9%). LC-MS m/z 342.1 (M+1).
(Z)-5-((2-((2-(1H-indol-3-yl)ethyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 2-(1H-indol-3-yl)-N-methylethanamine (8.3 mg, 39.9 mg theoretical, 20.8%). LC-MS m/z 380.4 (M+1).
(Z)-5-((2-((1,2,3,4-tetrahydroquinolin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 1,2,3,4-tetrahydroquinolin-3-amine (5 mg, 37.2 mg theoretical, 13.5%). LC-MS m/z 354.1 (M+1).
Displacement/De-protection of Mono-Boc Diamines
(R,Z)-5-((2-(methyl(piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (R)-tert-butyl 3-(methylamino)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (3.1 mg, 55.9 mg theoretical, 5.5%). LC-MS m/z 320.1 (M+1).
(S,Z)-5-((2-(methyl(piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (S)-tert-butyl 3-(methylamino)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (3.2 mg, 55.9 mg theoretical, 5.7%). LC-MS m/z 320.1 (M+1).
(S,Z)-5-((2-(piperidin-3-ylamino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (R)-tert-butyl 3-aminopiperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (6.9 mg, 32.1 mg theoretical, 21.5%). LC-MS m/z 306.1 (M+1).
(R,Z)-5-((2-(piperidin-3-ylamino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (S)-tert-butyl 3-aminopiperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (3.8 mg, 32.1 mg theoretical, 11.8%). LC-MS m/z 306.1 (M+1).
(Z)-5-((2-((piperidin-2-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 2-(aminomethyl)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (10.7 mg, 45.6 mg theoretical, 23.5%). LC-MS m/z 320.1 (M+1).
(Z)-5-((2-((piperidin-4-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 4-(aminomethyl)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (5.3 mg, 33.5 mg theoretical, 15.8%). LC-MS m/z 320.1 (M+1).
(R,Z)-5-((2-((piperidin-3-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (S)-tert-butyl 3-(aminomethyl)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (7.3 mg, 33.5 mg theoretical, 21.8%). LC-MS m/z 320.1 (M+1).
(Z)-5-((2-(methyl(piperidin-3-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 3-((methylamino)methyl)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (21.6 mg, 35 mg theoretical, 61.7%). LC-MS m/z 334.1 (M+1).
(Z)-5-((2-(3-((methylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl methyl(piperidin-3-ylmethyl)carbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (17.9 mg, 35 mg theoretical, 51.1%). LC-MS m/z 334.1 (M+1).
(Z)-5-((2-(methyl(piperidin-4-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 4-((methylamino)methyl)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (6.5 mg, 35 mg theoretical, 18.6%). LC-MS m/z 334.1 (M+1).
(S,Z)-5-((2-((piperidin-3-ylmethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (R)-tert-butyl 3-((methylamino)methyl)piperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (11.2 mg, 33.5 mg theoretical, 33.4%). LC-MS m/z 320.1 (M+1).
(Z)-5-((2-((2-aminoethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl (2-aminoethyl)carbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (10.7 mg, 27.9 mg theoretical, 38.4%). LC-MS m/z 266.1 (M+1).
(Z)-5-((2-(3-(methylamino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl methyl(piperidin-3-yl)carbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (26.9 mg, 33.5 mg theoretical, 80%). LC-MS m/z 320.1 (M+1).
(Z)-5-((2-(octahydro-1,5-naphthyridin-1(2H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl octahydro-1,5-naphthyridine-1(2H)-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (7.2 mg, 36.3 mg theoretical, 19.8%). LC-MS m/z 346.1 (M+1).
(Z)-5-((2-((3-aminobenzyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl (3-(aminomethyl)phenyl)carbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (6.5 mg, 28.7 mg theoretical, 22.7%). LC-MS m/z 328.1 (M+1).
(Z)-5-((2-((5-phenylpiperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 3-amino-5-phenylpiperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (5.6 mg, 33.4 mg theoretical, 16.8%). LC-MS m/z 382.1 (M+1).
(Z)-5-((2-((4-phenylpiperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 3-amino-4-phenylpiperidine-1-carboxylate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (5.7 mg, 33.4 mg theoretical, 17.1%). LC-MS m/z 382.1 (M+1).
(Z)-5-((2-((3-(aminomethyl)benzyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and tert-butyl 3-(aminomethyl)benzylcarbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (16.6 mg, 35.8 mg theoretical, 46.3%). LC-MS m/z 342.1 (M+1).
(Z)-5-((2-(octahydro-1,5-naphthyridin-1(2H)-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and 3-((tert-butoxycarbonyl)amino)-3-(piperidin-4-yl)propanoic acid. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (24.6 mg, 11.8 mg theoretical, 208%). LC-MS m/z 378.4 (M+1).
(S,Z)-5-((2-(3-aminopiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (S)-tert-butyl piperidin-3-ylcarbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (46.8 mg, 30.2 mg theoretical, 155%). LC-MS m/z 306.1 (M+1).
(R,Z)-5-((2-(3-aminopiperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general displacement procedure and (R)-tert-butyl piperidin-3-ylcarbamate. The crude protected amine was then treated with 2 mL DCE and 500 μL of TFA and shaken for 24 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residues were purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) (44.2 mg, 30.2 mg theoretical, 146%). LC-MS m/z 306.1 (M+1).
(Z)-5-β6-(methyl(piperidin-3-yl)amino)-2-(piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using General Procedure 2 for the Preparation of Amino-Analogs (Example 81) using tert-butyl 3-(methylamino)piperidine-1-carboxylate and piperidine (11.4 mg, 54.0 mg theoretical, 21.1%). LC-MS m/z 403.2 (M+1).
(Z)-5-((2-(methyl(piperidin-3-yl)amino)-6-(piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using General Procedure 2 for the Preparation of Amino-Analogs (Example 81) using piperidine and tert-Butyl 3-(methylamino)piperidine-1-carboxylate (10.5 mg, 26.3 mg theoretical, 41.9%). LC-MS m/z 403.2 (M+1).
(Z)-5-((2,6-di(piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using General Procedure 2 for the Preparation of Amino-Analogs (Example 81) using piperidine (14.0 mg, 233 mg theoretical, 6%). LC-MS m/z 374.2 (M+1).
(Z)-5-((2-(4-(aminomethyl)piperidin-1-yl)-6-(trifluoromethyl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared as follows.
A 30 mL round-bottomed vial was charged with 1,1,1-trifluoropentane-2,4-dione (2.00 g, 13.0 mmol, 1 equiv.), ethanol (15 mL, 0.8 M), thiomethylisourea hemi sulfuric acid salt (1.807 g, 6.5 mmol, 1 equiv.) and the reaction mixture was shaken at 80° C. for 3 h. The solvent was concentrated under reduced pressure and the residue was partitioned between CH2Cl2 (25 mL) and saturated NaHCO3 (25 mL). The aqueous layer was extracted with EtOAc (2×10 mL) and the combined organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide the crude desired pyrimidine as a slightly orange solid. Purification using the Biotage (SiO2, 25 g cartridge, Hexanes/EtOAc 95:5 to 75:25) afforded 1.66 g of the pure desired product (2.70 g theoretical, 61.4%). LC-MS m/z 209 (M+1).
A 30 mL round-bottomed vial was charged with 4-methyl-2-(methylthio)-6-(trifluoromethyl)pyrimidine (0.500 g, 2.4 mmol, 1 equiv.), ethanol (5 mL, 0.48 M), selenium dioxide (0.293 mg, 2.6 mmol, 1.1 equiv.), and the reaction mixture was shaken at 90° C. for 40 h and then RT for 14 d. The crude reaction mixture was then treated with thiazolidine-2,4-dione (0.281 g, 2.4 mmol, 1 equiv.), triethylamine (1.0 mL, 7.20 mmol, 3 equiv.) and the reaction mixture was shaken for 16 h at 80° C. The solvent was concentrated under reduced pressure and the residue was partitioned between EtOAc (30 mL) and saturated NaHCO3 (25 mL). The aqueous layer was extracted with EtOAc (2×10 mL) and the combined organic layer was dried over Na2SO4 and concentrated under reduced pressure. The crude product was purified using the Biotage (SiO2, 10 g cartridge, CH2Cl2/MeOH 99:1 to 9:1) that afforded 270 mg of partially purified product that was re-purified using the Biotage (SiO2, 10 g cartridge, Hexanes/EtOAc 90:10 to 0:1 then CH2Cl2/MeOH 99:1 to 9:1) afforded 212 mg of yellow solid that was still not completely pure but was used directly in the next step without further purification.
An 8 mL round-bottomed vial was charged with the pyrimidine sulfide (212 mg, 0.66 mmol, 1 equiv.), CH2Cl2 (3 mL, 0.22 M), m-CPBA 50% by weight (0.683 g, 1.98 mmol, 3 equiv.) was added over a 1 min. period at RT. After 3.5 h, an additional 3 equivalents of m-CPBA 50% by weight (0.683 g, 1.98 mmol, 3 equiv.) was added and the reaction mixture was stirred at RT overnight. The resulting white solid was filtered and washed with CH2Cl2 and then with Et2O to provide 67 mg of an off-white solid (233 mg theoretical, 28.7%), which was used in the next step without further purification. LC-MS m/z 354 (M+1).
An 8 mL round-bottomed vial was charged with the 2-sulfone pyrimidine (67 mg, 0.19 mmol, 1 equiv.), DMSO (1 mL, 0.19M), tert-Butyl (piperidin-4-ylmethyl)carbamate (40.6 mg, 0.19 mmol, 1 equiv.), DIPEA (66 μL, 0.38 mmol, 2 equiv.), and the reaction mixture was stirred for 1 h at RT and then 50° C. for 3 h. The reaction was directly purified using reverse phase HPLC (2 injections of 500 μL, 12 min method, methanol/water gradient with 0.4% TFA) to afford the desired product (15.3 mg, 92.7 mg theoretical, 16.5%).
An 8 mL round-bottomed vial was charged with the CF3-pyrimidine (15.3 mg, 0.031 mmol, 1 equiv.), CH2Cl2 (1 mL, 0.03 M), TFA (0.5 mL, 6.5 mmol, 208 equiv.), and the reaction mixture was stirred for 1 h at RT. The solvent was concentrated under reduced pressure and the residue was dried under high vacuum. The residue was washed with ether (2×2 mL) and the yellow solid was dried under high vacuum overnight to afford (13.4 mg, 15.8 mg theoretical, 85%). LC-MS m/z 388.1 (M+1).
(Z)-5-((2-(4-(aminomethyl)piperidin-1-yl)-6-methoxypyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared as follows.
A 30 mL round-bottomed vial was charged with methyl 2,6-dichloropyrimidine-4-carboxylate (0.6 g, 2.9 mmol, 1 equiv.), methanol (6 mL, 0.97 M), K2CO3 (0.401 g, 2.9 mmol, 1 equiv.), and the reaction mixture was shaken at 65° C. for 1.5 h. The solvent was concentrated under reduced pressure and the residue was partitioned between EtOAc (25 mL) and H2O (25 mL) and the water layer was extracted with EtOAc (2×20 mL). The combined organic layer was dried over Na2SO4 and concentrated under reduced pressure to provide the crude chloropyrimidine (441 mg, 588 mg theoretical, 75%), which was used in the next step without further purification.
An 8 mL round-bottomed vial was charged with the 2-chloropyrimidine (150 mg, 0.74 mmol, 1.5 equiv.), methanol (1.5 mL, 0.49 M), tert-Butyl (piperidin-4-ylmethyl)carbamate (159 mg, 0.49 mmol, 1 equiv.), DIPEA (258 μL, 0.99 mmol, 2 equiv.), and the reaction mixture was shaken at 65° C. for 3 h. The solvent was concentrated under reduced pressure and the residue was partitioned between EtOAc (25 mL) and saturated NaHCO3 (10 mL). The organic layer was dried over Na2SO4 and dried under reduced pressure to provide the crude product. Purification using the Biotage (SiO2, 10 g cartridge, Hexanes/EtOAc 95:5 to 40:60) afforded the desired pyrimidine intermediate as a white solid (219 mg, 281 mg theoretical, 78%).
A 50 mL 2-neck round-bottomed flask was charged with the methyl ester intermediate (150 mg, 0.39 mmol, 1 equiv.), CH2Cl2 (2 mL, 0.195 M), and then DIBAL-H 1 M in CH2Cl2 (0.59 mL, 0.59 mmol, 1.5 equiv.) was added over a 4 minute period at −78° C. The reaction was then stirred for 1.5 h at −78° C. and for 1.5 h between −78° C. and RT. LC-MS showed mostly starting material so the reaction mixture was re-cooled to −78° C. and DIBAL-H (0.8 mL, 0.8 mmol, 2 equiv.) was added. LC-MS showed mostly starting material. The reaction mixture was stored at −20° C. for 3 d. The reaction mixture was cooled to −78° C. and treated with 1M DIBAL-H in hexanes (0.59 mL, 0.59 mmol, 1 equiv.) over a 5 min. period, which produced a white precipitate. After 2.5 h, another equivalent of DiBAL-H (1 M in Hexanes, 0.59 mL) was added over a 15 min. period at −78° C. The reaction was quenched at −78° C. after 35 min. with methanol (1 mL). The solvent were concentrated under reduced pressure and the residue was partitioned between CH2Cl2 (20 mL) and saturated NaHCO3 (20 mL). The organic layer was dried over Na2SO4 and the solvent was concentrated under reduced pressure to provide the crude product, which was used in the next step without further purification.
An 8 mL round-bottomed vial was charged with the crude aldehyde (0.2 mmol, estimated), ethanol (2 mL), thiazolidine-2,4-dione (23 mg, 0.2 mmol, 1 equiv.), triethylamine (56 μL, 0.4 mmol, 2 equiv.), purged with Ar, and the reaction mixture was shaken at 80° C. for 24 h. The crude mixture was purified using the Biotage (SiO2, 10 g cartridge, CH2Cl2/MeOH 99:1 to 94:6) afforded 113 mg of the partially purified product. The sample was re-purified using reverse phase HPLC (methanol/water 10-90%, 0.4% TFA, 3 equal injections) provided the pure product as a TFA salt (47.3 mg, 225 mg theoretical, 21%). LC-MS m/z 450 (M+1).
An 8 mL round-bottomed vial was charged with the MeO-pyrimidine boc protected amine (47.3 mg, 105 μmol, 1 equiv.), CH2Cl2 (1.3 mL, 0.08 M), TFA (0.5 mL, 6.5 mmol, 62 equiv.), and the reaction mixture was stirred for 1 h at RT. The solvents were concentrated under reduced pressure and the residue was re-dissolved in DMSO (0.9 mL) and purified by reverse phase HPLC (methanol/water with 0.4% TFA, 10-90% method, 2 injections of 500 μL) to provide as the TFA salt (43.9 mg, 48.8 mg theoretical, 90%). LC-MS m/z 350.1 (M+1).
Synthesized Pyridine Analogs
(Z)-5-((6-(piperidin-1-yl)pyridin-2-yl)methylene)thiazolidine-2,4-dione was prepared as follows.
A 30 mL round-bottomed vial was charged with thiazolidine-2,4-dione (300 mg, 2.56 mmol, 1 equiv.), toluene (5 mL, 0.5 M), 6-bromopicolinaldehyde (477 mg, 2.56 mmol, 1 equiv.), glacial acetic acid (22 μL, 0.256 mmol, 0.1 equiv.), piperidine (25 μL, 0.256 mmol, 0.1 equiv.), purged with Ar, and heated with shaking at 125° C. After heating for 16 h, the yellow reaction solution was pipeted away from the solid precipitate. The precipitate was washed with acetone (3×5 mL) and dried under high vacuum to afford the desired product as a solid (439 mg, 731 mg theoretical, 60%), which was used in the next step without further purification.
A 2 dram round-bottomed vial was charged with (Z)-5-((6-bromopyridin-2-yl)methylene)thiazolidine-2,4-dione (60 mg, 0.210 mmol, 1 equiv.), DMSO (1 mL, 0.08 M), diisopropylethylamine (34 μL, 0.2 mmol, 1 equiv.), and piperidine (21 μL, 0.21 mmol, 1 equiv.), and the reaction was heated with shaking at 110° C. for 24 h. The solvent was removed under reduced pressure (Genvac HT-4) and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as a modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide (Z)-5-((6-(piperidin-1-yl)pyridin-2-yl)methylene)thiazolidine-2,4-dione (7.9 mg, 60.9 mg theoretical, 12.9%). LC-MS m/z 290.1 (M+1).
Synthesized Reductive Amination Analogs
General Reductive Amination Procedure: A 2-dram round-bottomed vial was charged with the crude amine/TFA salt prepared using the general displacement procedure followed by the general TFA de-protection procedure (0.115 mmol), DCE (2 mL), DIPEA (6 eq. 0.690 mmol), DMF (1 mL), the aldehyde (1 equiv., 0.115 mmol), and the reaction mixture was shaken for 1 h at RT. The reaction mixture was then treated with NaBH(OAc)3 (2.5 equiv., 0.230 mmol) and the reaction was shaken 16 h at RT. The reaction mixture was then diluted with DCE (2 mL) and NaHCO3 (2 mL). The aqueous layer was back extracted with DCE (2×2 mL) and the combined organic layer was concentrated under reduced pressure (Genevac HT-4) and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to afford the pure products as the TFA salt.
(Z)-5-((2-((2-(dimethylamino)ethyl)(methyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and picolinaldehyde (16.1 mg, 47 mg theoretical, 34.3%). LC-MS m/z 448.5 (M+1).
(Z)-5-((2-((2-((3-chlorobenzyl)amino)ethyl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the general General Reductive Amination Procedure (Example 169) and 3-chlorobenzaldehyde (5.6 mg, 40.9 mg theoretical, 13.7%). LC-MS m/z 390.8 (M+1).
(Z)-5-((2-(4-(((pyridin-2-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and picolinaldehyde (8.5 mg, 71.8 mg theoretical, 11.8%). LC-MS m/z 411.5 (M+1).
(S,Z)-5-((2-((1-(pyridin-2-ylmethyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and picolinaldehyde (2.6 mg, 34.7 mg theoretical, 7.1%). LC-MS m/z 397.1 (M+1).
(Z)-5-((2-(4-((((6-methylpyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-methylpicolinaldehyde (10.4 mg, 74.3 mg theoretical, 14%). LC-MS m/z 425.5 (M+1).
(Z)-5-((2-(4-((bis((6-methylpyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-methylpicolinaldehyde (2.5 mg, 92.6 mg theoretical, 2.7%). LC-MS m/z 530.6 (M+1).
(Z)-5-((2-(4-(((pyridin-3-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and nicotinaldehyde (5.3 mg, 71.8 mg theoretical, 7.4%). LC-MS m/z 411.5 (M+1).
(Z)-5-((2-(4-(((pyridin-4-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and isonicotinaldehyde (4.1 mg, 71.8 mg theoretical, 5.7%). LC-MS m/z 411.5 (M+1).
(S,Z)-5-((2-((1-(quinolin-2-ylmethyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and quinoline-2-carbaldehyde (2.2 mg, 78 mg theoretical, 2.8%). LC-MS m/z 447.5 (M+1).
(S,Z)-5-((2-((1-(isoquinolin-3-ylmethyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and isoquinoline-3-carbaldehyde (1.5 mg, 78 mg theoretical, 1.9%). LC-MS m/z 447.5 (M+1).
(Z)-5-((2-(4-(((quinolin-2-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and quinoline-2-carbaldehyde (3.8 mg, 81 mg theoretical, 4.7%). LC-MS m/z 461.5 (M+1).
(Z)-5-((2-(4-((((2-methylquinolin-4-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 2-methylquinoline-4-carbaldehyde (35.1 mg, 56.5 mg theoretical, 62.2%). LC-MS m/z 475.5 (M+1).
(Z)-5-((2-(4-(((isoquinolin-1-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and isoquinoline-1-carbaldehyde (35.1 mg, 43.8 mg theoretical, 80%). LC-MS m/z 461.5 (M+1).
(Z)-5-((2-(4-((((6-methoxypyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-methoxypicolinaldehyde (37.5 mg, 52.4 mg theoretical, 71.5%). LC-MS m/z 441.5 (M+1).
(Z)-5-((2-(4-((((5-(trifluoromethyl)pyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 5-(trifluoromethyl)picolinaldehyde (23 mg, 56.9 mg theoretical, 40.4%). LC-MS m/z 479.5 (M+1).
(Z)-5-((2-(4-((((6-fluoropyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-fluoropicolinaldehyde (29.3 mg, 51 mg theoretical, 57.5%). LC-MS m/z 429.5 (M+1).
(Z)-5-((2-(4-((((2-(piperidin-1-yl)pyrimidin-5-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 2-(piperidin-1-yl)pyrimidine-5-carbaldehyde (40.1 mg, 47 mg theoretical, 80%). LC-MS m/z 495.5 (M+1).
(Z)-5-((2-(4-((((3-(trifluoromethyl)pyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 3-(trifluoromethyl)picolinaldehyde (44 mg, 45.5 mg theoretical, 97%). LC-MS m/z 479.5 (M+1).
(Z)-5-((2-(4-((((3-fluoropyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 3-fluoropicolinaldehyde (42.5 mg, 40.7 mg theoretical, 104%). LC-MS m/z 429.5 (M+1).
(Z)-5-((2-(4-((((8-methoxyquinolin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 8-methoxyquinoline-2-carbaldehyde (35.5 mg, 46.6 mg theoretical, 76%). LC-MS m/z 491.5 (M+1).
(Z)-5-((2-(4-((((8-fluoroquinolin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 8-fluoroquinoline-2-carbaldehyde (28.5 mg, 45.5 mg theoretical, 62.7%). LC-MS m/z 479.5 (M+1).
(Z)-5-((2-(4-((((6-fluoroquinolin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-fluoroquinoline-2-carbaldehyde (32.7 mg, 45.5 mg theoretical, 71.9%). LC-MS m/z 479.5 (M+1).
(Z)-5-((2-(4-((pyridin-2-ylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 2-chloroisonicotinaldehyde (19.6 mg, 42.3 mg theoretical, 46.4%). LC-MS m/z 445.5 (M+1).
(Z)-5-((2-(4-((((5-fluoropyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 5-fluoropicolinaldehyde (7.9 mg, 40.7 mg theoretical, 19.4%). LC-MS m/z 429.5 (M+1).
(Z)-5-((2-(4-(((quinolin-4-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and quinoline-4-carbaldehyde (24.6 mg, 43.8 mg theoretical, 56.2%). LC-MS m/z 461.5 (M+1).
(Z)-5-((2-(4-((((1,8-naphthyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 1,8-naphthyridine-2-carbaldehyde (6.9 mg, 43.8 mg theoretical, 15.7%). LC-MS m/z 462.5 (M+1).
(S,Z)-5-((2-(3-((quinolin-2-ylmethyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and quinoline-2-carbaldehyde (30.9 mg, 54.9 mg theoretical, 56.3%). LC-MS m/z 447.2 (M+1).
(S,Z)-5-((2-(3-(((6-fluoroquinolin-2-yl)methyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-fluoroquinoline-2-carbaldehyde (26.7 mg, 57.1 mg theoretical, 46.7%). LC-MS m/z 465.5 (M+1).
(S,Z)-5-((2-(3-(((8-methoxyquinolin-2-yl)methyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 8-methoxyquinoline-2-carbaldehyde (16.4 mg, 58.6 mg theoretical, 28%). LC-MS m/z 477.5 (M+1).
(R,Z)-5-((2-(3-((quinolin-2-ylmethyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169)e and quinoline-2-carbaldehyde (24.9 mg, 54.9 mg theoretical, 45.3%). LC-MS m/z 447.5 (M+1).
(R,Z)-5-((2-(3-(((6-fluoroquinolin-2-yl)methyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-fluoroquinoline-2-carbaldehyde (24.1 mg, 57.1 mg theoretical, 42.2%). LC-MS m/z 465.5 (M+1).
(R,Z)-5-((2-(3-(((8-methoxyquinolin-2-yl)methyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 8-methoxyquinoline-2-carbaldehyde (15.5 mg, 58.6 mg theoretical, 26.4%). LC-MS m/z 477.5 (M+1).
(R,Z)-5-((2-(3-(((2-methylquinolin-4-yl)methyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 2-methylquinoline-4-carbaldehyde (25 mg, 56.6 mg theoretical, 44.1%). LC-MS m/z 461.5 (M+1).
(S,Z)-5-((2-(3-(((2-methylquinolin-4-yl)methyl)amino)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 2-methylquinoline-4-carbaldehyde (30 mg, 56.6 mg theoretical, 53%). LC-MS m/z 461.5 (M+1).
(Z)-5-((2-(4-((((6-(4-fluorophenyl)pyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-(4-fluorophenyl)picolinaldehyde (26.5 mg, 36.3 mg theoretical, 72.9%). LC-MS m/z 505.5 (M+1).
(Z)-5-((2-(4-((((6-(thiophen-2-yl)pyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-(thiophen-2-yl)picolinaldehyde (15.2 mg, 35.5 mg theoretical, 42.9%). LC-MS m/z 493.5 (M+1).
(Z)-5-((2-(4-((((6-(benzo[d][1,3]dioxol-5-yl)pyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-(benzo[d][1,3]dioxol-5-yl)picolinaldehyde (25.8 mg, 38.2 mg theoretical, 67.5%). LC-MS m/z 531.5 (M+1).
(Z)-5-((2-(4-((((6-(thiophen-3-yl)pyridin-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and 6-(thiophen-3-yl)picolinaldehyde (32.5 mg, 35.5 mg theoretical, 92%). LC-MS m/z 493.5 (M+1).
(Z)-5-((2-(4-(((azetidin-2-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and tert-butyl 2-formylazetidine-1-carboxylate followed by the general TFA de-protection procedure (15.2 mg, 68 mg theoretical, 22.4%). LC-MS m/z 389.5 (M+1).
(Z)-5-((2-(4-(((pyrrolidin-3-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and tert-butyl 3-formylpyrrolidine-1-carboxylate followed by the general TFA de-protection procedure (17.1 mg, 70.4 mg theoretical, 24%). LC-MS m/z 403.5 (M+1).
(Z)-5-((2-(((3S)-1-(pyrrolidin-3-ylmethyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and tert-butyl 3-formylpyrrolidine-1-carboxylate followed by the general TFA de-protection procedure (2.7 mg, 34.0 mg theoretical, 7.9%). LC-MS m/z 389.2 (M+1).
(Z)-5-((2-(4-(((piperidin-3-ylmethyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination
Procedure (Example 169) and tert-butyl 3-formylpiperidine-1-carboxylate followed by the general TFA de-protection procedure (26.5 mg, 72.9 mg theoretical, 36.4%). LC-MS m/z 417.2 (M+1).
(Z)-5-((2-(((3S)-1-(azetidin-2-ylmethyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and tert-butyl 2-formylazetidine-1-carboxylate followed by the general TFA de-protection procedure (2.2 mg, 32.8 mg theoretical, 6.0%). LC-MS m/z 375.2 (M+1).
(Z)-5-((2-(((3S)-1-(piperidin-3-ylmethyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reductive Amination Procedure (Example 169) and tert-butyl 3-formylpiperidine-1-carboxylate followed by the general TFA de-protection procedure (4.5 mg, 35.3 mg theoretical, 11.9%). LC-MS m/z 403.2 (M+1).
General Reverse Reductive Amination Procedure: A 2-dram round-bottomed vial was charged with tert-butyl 4-formylpiperidine-1-carboxylate (0.7 mmol), the amine (1 equiv., 0.7 mmol), DCE (3 mL), and shaken for 1 h at RT. The reaction mixture was then treated with NaBH(OAc)3 (2 equiv., 1.4 mmol) and shaken for 16 h at RT. The reaction mixture was then washed with saturated NaHCO3 (3 mL) and the aqueous layer was back extracted with DCE (2×2 mL. The combined organic layer was concentrated under reduced pressure (GeneVac HT-4) and the crude residue was purified by HPLC using a MeOH/H2O gradient with TFA as the modifier. The resulting Boc-protected piperidine analog was treated with DCE (3 mL), TFA (0.5 mL), and shaken at RT for 2 h. The reaction mixture was concentrated under reduced pressure (GeneVac HT-4) and used in the general displacement procedure without further purification.
(Z)-5-((2-(4-((pyridin-3-ylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reverse Reductive Amination Procedure (Example 214) and pyridin-3-amine (15.5 mg, 41.7 mg theoretical, 37.2%). LC-MS m/z 397.5 (M+1).
(Z)-5-((2-(4-(((4-morpholinophenyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reverse Reductive Amination Procedure (Example 214) and 4-morpholinoaniline (12.5 mg, 50.5 mg theoretical, 24.7%). LC-MS m/z 481.5 (M+1).
(Z)-5-((2-(4-((pyridin-2-ylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reverse Reductive Amination Procedure (Example 214) and pyridin-2-amine (21.2 mg, 41.7 mg theoretical, 50.9%). LC-MS m/z 397.5 (M+1).
(Z)-5-((2-(4-((((1H-benzo[d]imidazol-2-yl)methyl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reverse Reductive Amination Procedure (Example 214) and (1H-benzo[d]imidazol-2-yl)methanamine (8 mg, 42.7 mg theoretical, 18.7%). LC-MS m/z 450.5 (M+1).
(Z)-5-((2-(4-((quinolin-2-ylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using the General Reverse Reductive Amination Procedure (Example 214) and quinolin-2-amine (21.2 mg, 128 mg theoretical, 16.53%). LC-MS m/z 447.5 (M+1).
(Z)-N-(1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)pyrrolidin-3-yl)furan-2-carboxamide was prepared as follows.
A 2-dram round-bottomed vial was charged with (Z)-5-(2-(3-aminopyrrolidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione, prepared using the general displacement procedure followed by the general TFA de-protection procedure, (25 mg, 0.065 mmol), DCM (1 mL), furan-2-carbonyl chloride (8 μL, 0.082 mmol, 1.3 equiv.), and pyridine (0.040 mL, 0.491 mmol, 7.5 equiv.). The reaction mixture was shaken at RT for 16 h, the solvent was removed under reduced pressure (Genevac HT-4), and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide the title compound (2.7 mg, 33.1 mg theoretical, 8.2%). LC-MS m/z 386.1 (M+1).
(Z)-5-((2-(4-(furan-2-carbonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared as follows.
A 2-dram round-bottomed vial was charged with (Z)-5-((2-(1,4-diazepan-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione, prepared using the general displacement procedure followed by the general TFA de-protection procedure, (25 mg, 0.062 mmol), DCM (1 mL), furan-2-carbonyl chloride (8.07 μL, 0.062 mmol, 1 equiv.), and pyridine (0.040 mL, 0.491 mmol, 8 equiv.). The reaction mixture was shaken at RT for 16 h, the solvent was removed under reduced pressure (Genevac HT-4), and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide the title compound (1.9 mg, 32.7 mg theoretical, 5.8%). LC-MS m/z 400.1 (M+1).
(Z)-N-((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)pyrazine-2-carboxamide was prepared as follows.
A 2-dram round-bottomed vial was charged with (Z)-5-(2-(4-(aminomethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione, prepared using the general displacement procedure followed by the general TFA de-protection procedure, (56 mg, 0.175 mmol), DCM (3 mL), pyrazine-2-carbonyl chloride (25 mg, 0.175 mmol, 1 equiv.), and pyridine (0.120 mL, 1.47 mmol, 8.4 equiv.). The reaction mixture was shaken at RT for 16 h, the solvent was removed under reduced pressure (Genevac HT-4), and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide the title compound (4.9 mg, 74.5 mg theoretical, 6.6%). LC-MS m/z 426.5 (M+1).
(Z)-N-((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)-2,2,2-trifluoroacetamide was prepared as follows.
A 2-dram round-bottomed vial was charged with (Z)-5-(2-(4-(aminomethyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione, prepared using the general displacement procedure followed by the general TFA de-protection procedure, (56 mg, 0.175 mmol), DCM (3 mL), 2,2,2-trifluoroacetyl chloride (23 mg, 0.175 mmol, 1 equiv.), and pyridine (0.120 mL, 1.47 mmol, 8.4 equiv.). The reaction mixture was shaken at RT for 16 h, the solvent was removed under reduced pressure (Genevac HT-4), and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide the title compound (6.5 mg, 72.7 mg theoretical, 8.9%). LC-MS m/z 416.1 (M+1).
(S,Z)-5-((2-((1-(pyrazine-2-carbonyl)piperidin-3-yl)amino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared as follows.
A 2-dram round-bottomed vial was charged with (S,Z)-5-((2-(piperidin-3-ylamino)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione, prepared using the general displacement procedure followed by the general TFA de-protection procedure, (27 mg, 0.088 mmol), DCM (2 mL), pyrazine-2-carbonyl chloride (12.5 mg, 0.088 mmol, 1 equiv.), and pyridine (0.080 mL, 0.982 mmol, 11 equiv.). The reaction mixture was shaken at RT for 16 h, the solvent was removed under reduced pressure (Genevac HT-4), and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide the title compound (2.6 mg, 36.1 mg theoretical, 6.4%). LC-MS m/z 412.1 (M+1).
(Z)-3-amino-3-(1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)-N-(3-(trifluoromethoxy)benzyl)propanamide was prepared as follows.
A 2-dram round-bottomed vial was charged with (Z)-3-((tert-butoxycarbonyl)amino)-3-(1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)propanoic acid, prepared using the general displacement procedure, (25 mg, 0.052 mmol), DMF (1 mL), DIPEA (34.9 μL, 0.209 mmol, 4 equiv.), and (3-(trifluoromethoxy)phenyl)methanamine (7.85 μL, 0.052 mmol, 1 equiv.). The reaction mixture was shaken for 20 minutes then HBTU (29.8 mg, 0.079 mmol, 1.5 equiv.) was added and the reaction mixture was shaken at RT for 3 h. The solvent was removed under reduced pressure (Genevac HT-4) and the resulting solid was washed with water (2×1 mL) and dried under high vacuum to provide 20 mg of (Z)-tert-butyl (1-(1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)-3-oxo-3-(3-(trifluoromethoxy)benzyl)amino)propyl)carbamate (20 mg, 34.1 mg theoretical, 58.7%).
A 2-dram round-bottomed vial was charged with (Z)-tert-butyl (1-(1-(4-(2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)-3-oxo-3-((3-(trifluoromethoxy)benzyl)amino)propyl)carbamate (20 mg, 0.031 mmol), DCM (0.5 mL), and TFA (0.5 mL). The reaction mixture was shaken at RT for 16 h. The solvent was removed under reduced pressure (Genevac HT-4) and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to provide the title compound (15.6 mg, 16.9 mg theoretical, 92%). LC-MS m/z 551.2 (M+1)
(Z)-methyl 2-(((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)amino)pyrimidine-4-carboxylate was prepared as follows.
Methyl 2-((piperidin-4-ylmethyl)amino)pyrimidine-4-carboxylate was prepared as follows: A 40 mL round-bottomed vial was charged with tert-butyl 4-(aminomethyl)piperidine-1-carboxylate (1.76 mmol, 1.1 equiv.), acetonitrile (4 mL), DiPEA (2.37 mmol, 1.5 equiv.), methyl 2,6-dichloropyrimidine-4-carboxylate (1.58 mmol, 1 equiv.), and then shaken at 85° C. for 72 h. The reaction mixture was concentrated under reduced pressure and purified on SiO2 using a Biotage and a 10-50% EtOAc/hexanes gradient to provide the desired protected amine (233 mg, 552 mg theoretical, 42%). Methyl 2-((piperidin-4-ylmethyl)amino)pyrimidine-4-carboxylate was prepared using the general TFA de-protection procedure and used directly in the general displacement procedure to provide the title compound (4 mg, 73.4 mg theoretical, 5%). LC-MS m/z 456.1 (M+1).
(Z)-5-((2-(4-((imidazo[1,2-b]pyridazin-6-ylamino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using a procedure similar to the procedure used in the synthesis of Example 226 to provide the title compound (12.2 mg, 45.9 mg theoretical, 26.6%). LC-MS m/z 437.5 (M+1).
(Z)-5-((2-(4-(((1H-benzo[d]imidazol-2-yl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using a procedure similar to the procedure used in the synthesis of Example 226 to provide the title compound (21.4 mg, 45.8 mg theoretical, 46.7%). LC-MS m/z 436.5 (M+1).
(Z)-5-((2-(4-(((7H-purin-6-yl)amino)methyl)piperidin-1-yl)pyrimidin-4-yl)methylene)thiazolidine-2,4-dione was prepared using a procedure similar to the procedure used in the synthesis of Example 226 to provide the title compound (12.7 mg, 41.6 mg theoretical, 30.6%). LC-MS m/z 438.5 (M+1).
General Procedure for the Preparation of Sulfonamides A 2-dram round-bottomed vial was charged with the appropriate sulfonyl chloride (0.072 mmol, 1 equiv.) in 0.5 mL of DMF, and then treated carefully with a solution of the appropriate amine intermediate, prepared using the general displacement procedure followed by the general TFA de-protection procedure, (0.072 mmol, 1 equiv.), DIPEA (0.288 mmol, 4 equiv.), and 1 mL of DMF. The reaction mixture was then shaken at room temperature overnight. The reaction mixture was partitioned between 2 mL DCE and 1 mL sat. NaHCO3 and the aqueous layer was extracted with DCE (2×2 mL). The combined organic layer was the concentrated under reduced pressure (Genevac HT-4) and the crude residue was purified using reverse phase HPLC (MS-triggered fraction collection) with an acetonitrile/water or methanol/water gradient and trifluoroacetic acid as the modifier. The pure fractions were then concentrated under reduced pressure (Genevac HT-4) to afford the sulfonamide analogs.
(Z)-N-((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)naphthalene-2-sulfonamide was prepared using a procedure similar to the general procedure described in Example 230 to provide the title compound (7.7 mg, 36.7 mg theoretical, 21%). LC-MS m/z 510.5 (M+1).
(Z)-N-((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)-6-methoxynaphthalene-2-sulfonamide was prepared using a procedure similar to the general procedure described in Example 230 to provide the title compound (15.2 mg, 38.9 mg theoretical, 39.1%). LC-MS m/z 540.5 (M+1).
(Z)-5-chloro-N-((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)naphthalene-2-sulfonamide was prepared using a procedure similar to the general procedure described in Example 230 to provide the title compound (9.2 mg, 39.2 mg theoretical, 23.5%). LC-MS m/z 545 (M+1).
(Z)-N-((1-(4-((2,4-dioxothiazolidin-5-ylidene)methyl)pyrimidin-2-yl)piperidin-4-yl)methyl)-1-methyl-1H-indole-5-sulfonamide was prepared using a procedure similar to the general procedure described in Example 230 to provide the title compound (13.2 mg, 36.9 mg theoretical, 35.8%). LC-MS m/z 513.5 (M+1).
Protocols for Kinase Activity Screening for CK1γ1(h), CK1γ2(h), CK1γ3(h), CK1δ(h) and CK1(y): Kinase screening was performed by Millipore UK Ltd. Kinase dilution buffer composition: 20 mM MOPS, 1 mM EDTA, 0.01% Brij-35, 5% Glycerol, 0.1% b-mercaptoethanol, 1 mg/mL BSA.
In a final reaction volume of 25 μL, the compound of interest (at the desired concentration) and the appropriate kinase (5-10 mU) were incubated with 8 mM MOPS pH 7.0, 0.2 mM EDTA, 200 μM KRRRALS(p)VASLPGL (SEQ ID NO:1), 10 mM magnesium acetate and [γ-33P-ATP] (specific activity approx. 500 cpm/pmol, concentration as required). The reaction was initiated by the addition of the MgATP mix. After incubation for 40 minutes at room temperature, the reaction was stopped by the addition of 5 μL of a 3% phosphoric acid solution. 10 μL of the reaction mixture was then spotted onto a P30 filtermat; and washed three times for 5 minutes in 75 mM phosphoric acid, and once in methanol prior to drying and scintillation counting. The estimated IC50 values for several compounds are provided in Table 5.
The relative activity of the kinase as a function of the concentration of the compounds are depicted in
Additional IC50s for CK1 are shown in Table 6:
Additional % activity data is shown in Table 7.
PIM kinase assays were performed by Millipore UK Ltd. IC50 data is summarized in Table 8, and percent activity data is summarized in Table 9.
Additional percent activity data at 10 micromolar (μM) for compounds 4981 and 4991 is depicted in Tables 10 and 11.
Inhibition of PC-3 Cells:
Results are shown in Table 12:
Inhibition of OVCAR-3 Cells
Results are shown in Table 13:
Inhibition of LNCaP Cells
Results are shown in Table 14:
Inhibition of Jurkat Cells
Results are shown in Table 15:
Inhibition of MDA-MB-468 Cells
Results are shown in Table 16:
Inhibition of HCT116 Cells
Results are shown in Table 17:
Inhibition of A549 Cells
Results are shown in Table 18:
Inhibition of DU145 Cells
Results are shown in Table 19:
Inhibition of HCC1954 Cells
Results are shown in Table 20:
Inhibition of Caco-2 Cells
Results are shown in Table 21:
IC50 determination of compound 4991 against three cancer cell lines
Additional cell inhibition studies were performed by Crown Biosciences. The materials are described in Table 22.
The dose response curves of compound 4991 compared to cisplatin, as well as the calculated IC50 values, are shown in
In vitro ADME assays of PAMPA and human and rat hepatic microsomal stability.
The generic gradient HPLC and MS method summarized in Table 22 was used for the analysis of compounds 4981, 4985, 4991 and 4999.
Parallel artificial membrane permeability assays (PAMPA) were performed with the compounds 4981, 4985, 4991 and 4999. The target concentration in the assay was 10 μM, prepared by diluting (1000-fold) the 10 mM stock solutions in DMSO into PBS, pH 7.4. The final DMSO concentration was 0.1%. The 10 μM solutions were added, 300 μL, to wells in the donor plate. The receiver plate, which contained 200 μL of PBS, pH 7.4 per well, was placed in the donor plate and the assembly was incubated for 5 hours at ambient temperature. At the end of the incubation period the plates were separated and the compound concentrations in each solution were determined by LC/MS/MS. The assay was performed in triplicate. Dexamethasone and verapamil were used as reference compounds. The permeability, Pe, and mass retention, R, of each compound were calculated using the following equations, and the results are summarized in Table 17. The results for dexamethsone and verapamil were consistent with historical data.
Where:
Hepatic microsomal assays were performed with 4981, 4985, 4991 and 4999 in human and rat (Sprague-Dawley). Protein concentrations of 0.4 (human) and 0.2 mg/mL (rat) with an NADPH regenerating cofactor system (2.6 mM NADP+, 6.6 mM glucose-6-phosphate, 0.8 U/mL glucose-6-phosphate dehydrogenase, and 6.6 mM magnesium chloride) were used. A 100 μM 20% DMSO/80% acetonitrile working stock of each of the compounds was diluted 100 fold resulting in 1 μM compound/1% final organic reaction concentrations. Time points were removed at 0 and 60 minutes. At each time point, 100 μL of the incubation suspension was added to 200 μL of acetonitrile containing internal standard (tolbutamide), followed by centrifugation at 3,220 rcf for 10 minutes. Two hundred (200)μL of the resulting supernatants were removed, dried under nitrogen and reconstituted in 100 μL of 2 mM ammonium acetate, 0.1% formic acid in 50% methanol prior to analysis by LC/MS/MS. Testosterone and dexamethasone were used as reference compounds. Table 25 summarizes the results. The results for testosterone and dexamethasone were consistent with historical data.
Materials used are summarized in Table 26.
LC/MS Equipment:
Selected Cell Proliferation Inhibition Data
Cell Lines:
All cells were cultured in media supplemented with 10% FBS except for which are marked specially, in the temperature of 37° C., 5% CO2 and 95% humidity. All culture media were purchased from GIBCO (USA, IMDM Cat. 12200-036; RPMI Medium 1640 Cat. 31800-022; 2-mercaptoethanol Cat. 21985-023).
Reagents:
0.92 mg/mL PMS in DPBS Filter-sterilize through a 0.2 m filter into a sterile, lig0ht-protected container. Store at −20° C.
Preparation of MTS Solution:
The following protocol is recommended for the preparation of 21 mL of MTS solution (sufficient for ten 96-well plates).
SpectraMAX plus microplate spectrophotometer Model 3011, Molecular Devices Corp. (California, USA); CO2 water jacketed incubator, Therma (USA). Reverse microscope, Chongguang XDS-1B, Chongqing Guangdian Corp. (Chongqing, P.R. China).
Cytotoxicity and IC50 Determination:
The software of GraphPad Prism version 5 was used to calculate IC50. The graphical curves were fitted using a nonlinear regression model with a sigmoidal dose.
Results
Results are shown in Tables 27 and 28.
All of the U.S. patents and U.S. published patent applications cited herein are hereby incorporated by reference.
While several embodiments of the present invention have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the functions and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the present invention. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the teachings of the present invention is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, the invention may be practiced otherwise than as specifically described and claimed. The present invention is directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the scope of the present invention.
This application is a divisional of U.S. patent application Ser. No. 12/978,089 filed Dec. 23, 2010, which claims the benefit of priority to U.S. Provisional Patent Application Ser. No. 61/289,685, filed Dec. 23, 2009; and U.S. Provisional Patent Application Ser. No. 61/324,481, filed Apr. 15, 2010.
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| Number | Date | Country | |
|---|---|---|---|
| 20140080799 A1 | Mar 2014 | US |
| Number | Date | Country | |
|---|---|---|---|
| 61289685 | Dec 2009 | US | |
| 61324481 | Apr 2010 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12978089 | Dec 2010 | US |
| Child | 14032739 | US |
