PDK1 inhibitors and methods for making and using the same

Abstract

In accordance with the purpose(s) of the present disclosure, described herein are pyruvate dehydrogenase kinase 1 (PDK1) inhibitors and methods for treating cancer in a subject. In one aspect, the compounds having a formula represented by structure I or the pharmaceutically acceptable salt thereof as provided herein can be used to treat cancer associated with an elevated level of PDK1 in the subject such as, for example, glioblastoma, medulloblastoma, or breast cancer. Pharmaceutical compositions composed of the PDK1 inhibitors described herein are also provided.

Description

ATTORNEY DOCKET NO. 320903-2580PDK1 INHIBITORS AND METHODS FOR MAKING AND USING THE SAMECROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of and priority to co-pending U. S. Provisional Patent Application No. 63 / 742,623, filed on January 7, 2025, the contents of which are incorporated by reference herein in its entirety.BACKGROUND

[0002] Glioblastoma multiforme (GBM) is recognized as the most common primary malignant brain tumor exhibiting a uniformly lethal nature [1-3], The current standard treatment for GBM involves maximal surgical resection, followed by concurrent chemoradiotherapy and maintenance chemotherapy [4], Despite advanced treatments, the median survival is 14-16 months, with survival rates falling below 3% [5], Notably, GBM is the second leading cause of cancer-related deaths in males aged 20-39 and ranks fifth for women [6], The incidence rate in the United States is about 3.19 per 100,000, with a median age of diagnosis at 64 years. With a dismal long-term prognosis for GBM patients, it is essential to emphasize that primary brain cancers rank first in the average years of life lost among all cancers [7, 8], GBM is characterized by significant heterogeneity at the histopathological and molecular levels [9, 10], However, this heterogeneity presents substantial challenges in treatment effectiveness due to therapeutic resistance and complications in developing targeted therapies.SUMMARY

[0003] In accordance with the purpose(s) of the present disclosure, described herein are pyruvate dehydrogenase kinase 1 (PDK1) inhibitors and methods for treating cancer in a subject. In one aspect, the compounds having a formula represented by structure I or the pharmaceutically acceptable salt thereof as provided herein can be used to treat cancer associated with an elevated level of PDK1 in the subject such as, for example, glioblastoma, medulloblastoma, or breast cancer. Pharmaceutical compositions composed of the PDK1 inhibitors described herein are also provided.

[0004] Other systems, methods, features, and advantages of the present disclosure will be or become apparent to one with skill in the art upon examination of the following drawings and detailed description. It is intended that all such additional systems, methods, features, and advantages be included within this description, be within the scope of the present disclosure, andATTORNEY DOCKET NO. 320903-2580be protected by the accompanying claims. In addition, all optional and preferred features and modifications of the described embodiments are usable in all aspects of the disclosure taught herein. Furthermore, the individual features of the dependent claims, as well as all optional and preferred features and modifications of the described embodiments are combinable and interchangeable with one another.BRIEF DESCRIPTION OF THE DRAWINGS

[0005] Many aspects of the present disclosure can be better understood with reference to the following drawings. The components in the drawings are not necessarily to scale, emphasis instead being placed upon clearly illustrating the principles of the present disclosure. Moreover, in the drawings, like reference numerals designate corresponding parts throughout the several views.

[0006] FIGS. 1A-1J provide exemplary synthetic schemes for synthesizing the compounds described herein.

[0007] FIGS. 2A-2Z provide exemplary synthetic schemes for synthesizing the compounds described herein.

[0008] FIGS. 3A-3J provide exemplary synthetic schemes for synthesizing the compounds described herein.

[0009] FIGS. 4A-4E provide MTT assays with dose-dependent reduction in cell viability upon JVK-1206 treatment. U87 cells were treated with varying concentrations of JVK-1026 (A, B) or DCA (C), and cell viability was assessed using the MTT assay. (A) A dose-dependent reduction in cell viability was observed with JVK-1026, with significant decreases at 0.5 mM, 1 mM, and 2.5 mM concentrations (Cell count = 10000 cells / well; n - 6). (B) Lower concentrations of JVK-1026 (25 pM to 200 pM) also showed a significant reduction in cell viability, with a 50% reduction at 100 pM (Cell count = 20000 cells / well; n = 6). (C) DCA treatment at similar concentrations did not significantly reduce cell viability compared to control (Cell count = 20000 cells / well; n = 6). Astrocytes were treated with JVK-1026 (D) or DCA (E) at 100 pM and 200 pM concentrations. No significant changes in cell viability were observed in astrocytes, indicating that both compounds do not exhibit neurotoxic effects at these concentrations (Cell count = 20000 cells / well; n = 6).

[0010] FIGS. 5A-5C show cell cycle analysis of U87 cells and astrocytes. (A) U87 cells treated with JVK-1026 showed significant changes in cell cycle distribution, with a reduction in the G0 / G1 phase (p = 0.02) and an increase in both the S phase (p = 0.005) and G2 / M phase (p = 0.002),ATTORNEY DOCKET NO. 320903-2580indicating cell cycle arrest at the G2 / M phase. (B) In contrast, DCA treatment of U87 cells did not result in significant changes in cell cycle distribution compared to control. (C) Astrocytes treated with JVK-1026 showed no significant alterations in cell cycle distribution, suggesting that JVK-1026 selectively affects glioblastoma cells without impacting non-cancerous astrocytes.

[0011] FIGS. 6A-6B show JVK-1026 reduces PDK1 expression and enhances mitochondrial metabolism in U87 cells. (A) U87 cells treated with JVK-1026 (100 pM) for 48 hours shows the expression profile of PDK1, EGFR, and pEGFR. GAPDH was used as a loading control. Densitometry analysis was performed using ImageJ software, and results are shown as arbitrary units (n = 3). (B) RT-PCR analysis of PDH, a-KG, and CS in response to JVK-1026 treatment.

[0012] FIGS. 7A-7D show JVK-1026 inhibits glycolysis in U87 cells. (A) U87 cells (40,000 cells / well) were treated with 100 pM JVK-1026, and ECAR was measured over time to assess glycolytic activity. The control group (red) exhibited higher ECAR levels compared to JVK-1026-treated cells (blue), indicating a significant reduction in glycolytic flux following JVK-1026 treatment. The data represent the mean ± SEM from three independent experiments (n = 3) (B) Quantification of ECAR data from panel A shows that JVK-1026 significantly reduced glycolysis and glycolytic capacity in U87 cells compared to the control group (C) ROS production was measured in U87 cells treated with 100 pM JVK-1026 using a fluorescence-based assay. Data are shown as relative fold change ± SEM from three independent experiments (n = 3) (D) Lactate levels were measured in the culture media of U87 cells treated with 100 pM JVK-1026 to assess glycolytic output. JVK-1026 treatment significantly reduced lactate release compared to control cells (p = 0.001), further confirming the inhibition of glycolysis by JVK-1026. Data are presented as mean ± SEM from three independent experiments (n = 3).

[0013] FIG. 8 shows JVK-1026 inhibits U87 cell migration. Quantification of wound closure shows that JVK-1026 treatment resulted in a more pronounced inhibition of migration compared to DCA (n = 3).

[0014] FIG. 9 shows JVK-1026 inhibits U87 cell invasion. U87 cells were treated with 100 pM JVK-1026 or 100 pM DCA for 24 hours, and cell invasion was assessed using a transwell invasion assay as described previously. Quantification (right panel) reveals that JVK-1026 reduced invasion by approximately 83%, while DCA treatment resulted in a moderate reduction of around 50% (n - 4). Data are presented as mean ± SEM, with individual data points shown.

[0015] FIGS. 10A-10B show JVK-1026 enhances survival and reduces tumor burden in the U87 GBM mouse model. (A) Athymic nude mice implanted with 80,000 U87 GBM cells wereATTORNEY DOCKET NO. 320903-2580randomized on day 13 and treated with either vehicle (DMSO) or 1 mg JVK-1026. Kaplan-Meier survival analysis shows that JVK-1026 significantly prolonged survival compared to the vehicle-treated group (B) Vehicle-treated mice experienced rapid weight loss starting around day 15, correlating with tumor progression. In contrast, JVK-1026-treated mice maintained stable weights until day 20, after which a gradual decline was observed, indicating delayed tumor-associated weight loss.

[0016] FIG. 11 shows JVK-1025 and JVK-1026 disrupt apoptosis in vitro (U87 cell lines).

[0017] FIGS. 12A-12D show the / n v / tro efficacy of J VK 1009 targeting PDK1 in medulloblastoma.

[0018] Additional advantages of the invention will be set forth in part in the description which follows, and in part will be obvious from the description, or can be learned by practice of the invention. The advantages of the invention will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention, as claimed.DETAILED DESCRIPTION

[0019] Many modifications and other embodiments disclosed herein will come to mind to one skilled in the art to which the disclosed compositions and methods pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the disclosures are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. The skilled artisan will recognize many variants and adaptations of the aspects described herein. These variants and adaptations are intended to be included in the teachings of this disclosure and to be encompassed by the claims herein.

[0020] Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

[0021] As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present disclosure.

[0022] Any recited method can be carried out in the order of events recited or in any other order that is logically possible. That is, unless otherwise expressly stated, it is in no way intended thatATTORNEY DOCKET NO. 320903-2580any method or aspect set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not specifically state in the claims or descriptions that the steps are to be limited to a specific order, it is no way intended that an order be inferred, in any respect. This holds for any possible non-express basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, or the number or type of aspects described in the specification.

[0023] All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and / or materials in connection with which the publications are cited. The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided herein can be different from the actual publication dates, which can require independent confirmation.

[0024] While aspects of the present disclosure can be described and claimed in a particular statutory class, such as the system statutory class, this is for convenience only and one of skill in the art will understand that each aspect of the present disclosure can be described and claimed in any statutory class.

[0025] It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosed compositions and methods belong. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the specification and relevant art and should not be interpreted in an idealized or overly formal sense unless expressly defined herein.

[0026] Prior to describing the various aspects of the present disclosure, the following definitions are provided and should be used unless otherwise indicated. Additional terms may be defined elsewhere in the present disclosure.Definitions

[0027] As used herein, “comprising” is to be interpreted as specifying the presence of the statedATTORNEY DOCKET NO. 320903-2580features, integers, steps, or components as referred to, but does not preclude the presence or addition of one or more features, integers, steps, or components, or groups thereof. Moreover, each of the terms “by,” “comprising,” “comprises,” “comprised of,” “includes,” “included,” “involving,” “involves,” “involved,” and “such as” are used in their open, non-limiting sense and may be used interchangeably. Further, the term “comprising” is intended to include examples and aspects encompassed by the terms “consisting essentially of and “consisting of.” Similarly, the term “consisting essentially of” is intended to include examples encompassed by the term “consisting of.

[0028] As used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an excipient” includes, but is not limited to, mixtures or combinations of two or more such excipients, and the like.

[0029] It should be noted that ratios, concentrations, amounts, and other numerical data can be expressed herein in a range format. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. Ranges can be expressed herein as from “about” one particular value, and / or to “about” another particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms a further aspect. For example, if the value “about 10” is disclosed, then “10” is also disclosed.

[0030] When a range is expressed, a further aspect includes from the one particular value and / or to the other particular value. For example, where the stated range includes one or both limits, ranges excluding either or both of those included limits are also included in the disclosure, e g. the phrase “x to y” includes the range from ‘x’ to ‘y’ as well as the range greater than ‘x’ and less than ‘y’. The range can also be expressed as an upper limit, e.g. ‘about x, y, z, or less’ and should be interpreted to include the specific ranges of ‘about x’, ‘about y’, and ‘about z’ as well as the ranges of ‘less than x’, less than y’, and ‘less than z’. Likewise, the phrase ‘about x, y, z, or greater’ should be interpreted to include the specific ranges of ‘about x’, ‘about y’, and ‘about z’ as well as the ranges of ‘greater than x’, greater than y’, and ‘greater than z’. In addition, the phrase “about ‘x’ to ‘y’”, where ‘x’ and ‘y’ are numerical values, includes “about ‘x’ to about ‘y’”.ATTORNEY DOCKET NO. 320903-2580

[0031] It is to be understood that such a range format is used for convenience and brevity, and thus, should be interpreted in a flexible manner to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or subranges encompassed within that range as if each numerical value and sub-range is explicitly recited. To illustrate, a numerical range of “about 0.1% to 5%” should be interpreted to include not only the explicitly recited values of about 0.1% to about 5%, but also include individual values (e.g., about 1%, about 2%, about 3%, and about 4%) and the sub-ranges (e.g., about 0.5% to about 1.1%; about 5% to about 2.4%; about 0.5% to about 3.2%, and about 0.5% to about 4.4%, and other possible sub-ranges) within the indicated range. Thus, for example, if a component is in an amount of about 1%, 2%, 3%, 4%, or 5%, where any value can be a lower and upper endpoint of a range, then any range is contemplated between 1% and 5% (e.g., 1% to 3%, 2% to 4%, etc.).

[0032] As used herein, the terms “about,” “approximate,” “at or about,” and “substantially” mean that the amount or value in question can be the exact value or a value that provides equivalent results or effects as recited in the claims or taught herein. That is, it is understood that amounts, sizes, formulations, parameters, and other quantities and characteristics are not and need not be exact, but may be approximate and / or larger or smaller, as desired, reflecting tolerances, conversion factors, rounding off, measurement error and the like, and other factors known to those of skill in the art such that equivalent results or effects are obtained. In some circumstances, the value that provides equivalent results or effects cannot be reasonably determined. In such cases, it is generally understood, as used herein, that “about” and “at or about” mean the nominal value indicated ±10% variation unless otherwise indicated or inferred. In general, an amount, size, formulation, parameter or other quantity or characteristic is “about,” “approximate,” or “at or about” whether or not expressly stated to be such. It is understood that where “about,” “approximate,” or “at or about” is used before a quantitative value, the parameter also includes the specific quantitative value itself, unless specifically stated otherwise.

[0033] As used herein, half maximal effective concentration (ECso) is a measure of the concentration of a drug, antibody or toxicant which induces a biological response halfway between the baseline and maximum after a specified exposure time.

[0034] A residue of a chemical species, as used in the specification and concluding claims, refers to the moiety that is the resulting product of the chemical species in a particular reaction scheme or subsequent formulation or chemical product, regardless of whether the moiety is actuallyATTORNEY DOCKET NO. 320903-2580obtained from the chemical species. Thus, an ethylene glycol residue in a polyester refers to one or more -OCH2CH2O- units in the polyester, regardless of whether ethylene glycol was used to prepare the polyester. Similarly, a sebacic acid residue in a polyester refers to one or more -CO(CH2)8CO- moieties in the polyester, regardless of whether the residue is obtained by reacting sebacic acid or an ester thereof to obtain the polyester.

[0035] As used herein, the term “substituted” is 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, and aromatic and nonaromatic substituents of organic compounds. Illustrative substituents include, for example, those described below. The permissible substituents can be one or more and the same or different for appropriate organic compounds. For purposes of this disclosure, the heteroatoms, such as nitrogen, can have hydrogen substituents and / or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. This disclosure is not intended to be limited in any manner by the permissible substituents of organic compounds. Also, the terms “substitution” or “substituted with” include 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., a compound that does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc. It is also contemplated that, in certain aspects, unless expressly indicated to the contrary, individual substituents can be further optionally substituted ( / .e., further substituted, or unsubstituted).

[0036] The position of a substituent can be defined relative to the positions of other substituents in an aromatic ring. For example, as shown below in relationship to the “R” group, a second substituent can be “ortho,” “para,” or “meta” to the R group, meaning that the second substituent is bonded to a carbon labeled ortho, para, or meta as indicated below. Combinations of ortho, para, and meta substituents relative to a given group or substituent are also envisioned and should be considered to be disclosed.orthoparaATTORNEY DOCKET NO. 320903-2580

[0037] In defining various terms, “A1,” “A2,” “A3,” and “A4” are used herein as generic symbols to represent various specific substituents. These symbols can be any substituent, not limited to those disclosed herein, and when they are defined to be certain substituents in one instance, they can, in another instance, be defined as some other substituents.

[0038] The term “aliphatic” or “aliphatic group,” as used herein, denotes a hydrocarbon moiety that may be straight-chain ( / .e., unbranched), branched, or cyclic (including fused, bridging, and spirofused polycyclic) and may be completely saturated or may contain one or more units of unsaturation, but which is not aromatic. Unless otherwise specified, aliphatic groups contain 1-20 carbon atoms. Aliphatic groups include, but are not limited to, linear or branched, alkyl, alkenyl, and alkynyl groups, and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl)alkyl or (cycloalkyl)alkenyl.

[0039] The term “alkyl” as used herein is a branched or unbranched saturated hydrocarbon group of 1 to 24 carbon atoms, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, s-butyl, t-butyl, n-pentyl, isopentyl, s-pentyl, neopentyl, hexyl, heptyl, octyl, nonyl, decyl, dodecyl, tetradecyl, hexadecyl, eicosyl, tetracosyl, and the like. The alkyl group can be cyclic or acyclic. The alkyl group can be branched or unbranched. The alkyl group can also be substituted or unsubstituted. For example, the alkyl group can be substituted with one or more groups including, but not limited to, alkyl, cycloalkyl, alkoxy, amino, ether, halide, hydroxy, nitro, silyl, sulfo-oxo, or thiol, as described herein. A “lower alkyl” group is an alkyl group containing from one to six (e.g., from one to four) carbon atoms. The term alkyl group can also be a C1 alkyl, C1-C2 alkyl, C1-C3 alkyl, C1-C4 alkyl, C1-C5 alkyl, C1-C6 alkyl, C1-C7 alkyl, C1-C8 alkyl, C1-C9 alkyl, C1-C10 alkyl, and the like up to and including a C1-C24 alkyl.

[0040] Throughout the specification “alkyl” is generally used to refer to both unsubstituted alkyl groups and substituted alkyl groups; however, substituted alkyl groups are also specifically referred to herein by identifying the specific substituent(s) on the alkyl group. For example, the term “halogenated alkyl” or “haloalkyl” specifically refers to an alkyl group that is substituted with one or more halide, e.g., fluorine, chlorine, bromine, or iodine. Alternatively, the term “monohaloalkyl” specifically refers to an alkyl group that is substituted with a single halide, e.g. fluorine, chlorine, bromine, or iodine. The term “polyhaloalkyl” specifically refers to an alkyl group that is independently substituted with two or more halides, i.e. each halide substituent need not be the same halide as another halide substituent, nor do the multiple instances of a halide substituent need to be on the same carbon.ATTORNEY DOCKET NO. 320903-2580

[0041] The term “alkoxyalkyl” specifically refers to an alkoxy group as defined herein attached to the parent molecular moiety through an alkylene group (e.g., (-CH2-)n).

[0042] The term “aminoalkyl” specifically refers to an amino group as defined herein attached to the parent molecular moiety through an alkylene group (e.g., (-CH2-)n).

[0043] The term “hydroxyalkyl” specifically refers to a hydroxy group as defined herein attached to the parent molecular moiety through an alkylene group (e.g., (-CH2-)n).

[0044] This practice is also used for other groups described herein. That is, while a term such as “cycloalkyl” refers to both unsubstituted and substituted cycloalkyl moieties, the substituted moieties can, in addition, be specifically identified herein; for example, a particular substituted cycloalkyl can be referred to as, e.g., an “alkylcycloalkyl.” Similarly, a substituted alkoxy can be specifically referred to as, e.g., a “halogenated alkoxy,” a particular substituted alkenyl can be, e.g., an “alkenylalcohol,” and the like. Again, the practice of using a general term, such as “cycloalkyl,” and a specific term, such as “alkylcycloalkyl,” is not meant to imply that the general term does not also include the specific term.

[0045] The term “cycloalkyl” or “cycloalkylene” as used herein is a non-aromatic carbon-based ring composed of at least three carbon atoms. Examples of cycloalkyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, norbornyl, and the like. The term “heterocycloalkyl” is a type of cycloalkyl group as defined above, and is included within the meaning of the term “cycloalkyl,” where at least one of the carbon atoms of the ring is replaced with a heteroatom such as, but not limited to, nitrogen, oxygen, sulfur, or phosphorus. The cycloalkyl group and heterocycloalkyl group can be substituted or unsubstituted. The cycloalkyl group and heterocycloalkyl group can be substituted with one or more groups including, but not limited to, alkyl, cycloalkyl, aryl, heteroaryl, alkoxy, amino, ether, halide, hydroxy, nitro, silyl, sulfooxo, or thiol as described herein.

[0046] The term “alkylene” as used herein, refers to a divalent saturated aliphatic group, with one or two saturated carbon atom(s) as the point(s) of attachment, a linear or branched, cyclo, cyclic or acyclic structure, no carbon-carbon double or triple bonds, and no atoms other than carbon and hydrogen. For example, the alkylene group can be represented by the formula -(CH2)n-, where n is an integer from 1 to 10. The groups, -CH2- (methylene), -CH2CH2-, -CH2C(CH3)2CH2-, and -CH2CH2CH2- are non-limiting examples of alkylene groups. A substituted alkylene group is when one of the hydrogen atoms of the alkylene group is replaced with another group such including,ATTORNEY DOCKET NO. 320903-2580but not limited to, alkyl, cycloalkyl, alkoxy, amino, ether, halide, hydroxy, nitro, silyl, sulfo-oxo, or thiol as described herein.

[0047] The terms “alkoxy” and “alkoxyl” as used herein to refer to an alkyl or cycloalkyl group bonded through an ether linkage; that is, an “alkoxy” group can be defined as — OA1where A1is alkyl or cycloalkyl as defined above. “Alkoxy” also includes polymers of alkoxy groups as just described; that is, an alkoxy can be a polyether such as — OA1— OA2or — OA1— (OA2)a— OA3, where “a” is an integer of from 1 to 200 and A1, A2, and A3are alkyl and / or cycloalkyl groups.

[0048] The term “aryloxy” as used herein to refer to an aryl group bonded through an ether linkage; that is, an “aryloxy” group can be defined as — OA1where A1is aryl as defined herein.

[0049] The term “alkenyl” as used herein is a hydrocarbon group of from 2 to 24 carbon atoms with a structural formula containing at least one carbon-carbon double bond. Asymmetric structures such as (A1A2)C=C(A3A4) are intended to include both the E and Z isomers. This can be presumed in structural formulae herein wherein an asymmetric alkene is present, or it can be explicitly indicated by the bond symbol C=C. The alkenyl group can be substituted with one or more groups including, but not limited to, alkyl, cycloalkyl, heterocycloalkyl, alkoxy, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, azide, nitro, silyl, sulfo-oxo, or thiol, as described herein.

[0050] The term “cycloalkenyl” as used herein is a non-aromatic carbon-based ring composed of at least three carbon atoms and containing at least one carbon-carbon double bound, i.e., C=C. Examples of cycloalkenyl groups include, but are not limited to, cyclopropenyl, cyclobutenyl, cyclopentenyl, cyclopentadienyl, cyclohexenyl, cyclohexadienyl, norbornenyl, and the like. The term “heterocycloalkenyl” is a type of cycloalkenyl group as defined above and is included within the meaning of the term “cycloalkenyl,” where at least one of the carbon atoms of the ring is replaced with a heteroatom such as, but not limited to, nitrogen, oxygen, sulfur, or phosphorus. The cycloalkenyl group and heterocycloalkenyl group can be substituted or unsubstituted. The cycloalkenyl group and heterocycloalkenyl group can be substituted with one or more groups including, but not limited to, alkyl, cycloalkyl, alkoxy, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, azide, nitro, silyl, sulfo-oxo, or thiol as described herein.

[0051] The term “alkynyl” as used herein is a hydrocarbon group of 2 to 24 carbon atoms with a structural formula containing at least one carbon-carbon triple bond. The alkynyl group can be unsubstituted or substituted with one or more groups including, but not limited to, alkyl, cycloalkyl,ATTORNEY DOCKET NO. 320903-2580alkoxy, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, azide, nitro, silyl, sulfo-oxo, or thiol, as described herein.

[0052] The term “cycloalkynyl” as used herein is a non-aromatic carbon-based ring composed of at least seven carbon atoms and containing at least one carbon-carbon triple bound. Examples of cycloalkynyl groups include, but are not limited to, cyclooctynyl, cyclononynyl, and the like. The term “heterocycloalkynyl” is a type of cycloalkenyl group as defined above and is included within the meaning of the term “cycloalkynyl,” where at least one of the carbon atoms of the ring is replaced with a heteroatom such as, but not limited to, nitrogen, oxygen, sulfur, or phosphorus. The cycloalkynyl group and heterocycloalkynyl group can be substituted or unsubstituted. The cycloalkynyl group and heterocycloalkynyl group can be substituted with one or more groups including, but not limited to, alkyl, cycloalkyl, alkoxy, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, azide, nitro, silyl, sulfo-oxo, or thiol as described herein.

[0053] The term “aromatic group” as used herein refers to a ring structure having cyclic clouds of delocalized IT electrons above and below the plane of the molecule, where the TT clouds contain (4n+2) TT electrons. A further discussion of aromaticity is found in Morrison and Boyd, Organic Chemistry, (5th Ed., 1987), Chapter 13, entitled “Aromaticity,” pages 477-497, incorporated herein by reference. The term “aromatic group” is inclusive of both aryl and heteroaryl groups.

[0054] The term “aryl” as used herein is a group that contains any carbon-based aromatic group including, but not limited to, benzene, naphthalene, phenyl, biphenyl, anthracene, and the like. The aryl group can be substituted or unsubstituted. The aryl group can be substituted with one or more groups including, but not limited to, alkyl, cycloalkyl, alkoxy, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, heteroaryl, aldehyde, — NH2, carboxylic acid, ester, ether, halide, hydroxy, ketone, azide, nitro, silyl, sulfo-oxo, or thiol as described herein. The term “biaryl” is a specific type of aryl group and is included in the definition of “aryl.” In addition, the aryl group can be a single ring structure or comprise multiple ring structures that are either fused ring structures or attached via one or more bridging groups such as a carbon-carbon bond. For example, biaryl to two aryl groups that are bound together via a fused ring structure, as in naphthalene, or are attached via one or more carbon-carbon bonds, as in biphenyl. Fused aryl groups including, but not limited to, indene and naphthalene groups are also contemplated.ATTORNEY DOCKET NO. 320903-2580

[0055] The term “aldehyde” as used herein is represented by the formula -C(O)H. Throughout this specification “C(O)” is a shorthand notation for a carbonyl group, i.e., C=O.

[0056] The terms “amine” or “amino” as used herein are represented by the formula -NH2.

[0057] The term “substituted amino group” is represented by the structure -NAW, where A1and A2can be, independently, hydrogen or alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein, and wherein both A1and A2are not hydrogen. Representative examples include, but are not limited to, methylamino group, ethylamino group, propylamino group, isopropylamino group, butylamino group, isobutylamino group, (sec-butyl)amino group, (te / T-butyl)amino group, pentylamino group, isopentylamino group, (tert-pentyl)amino group, hexylamino group, dimethylamino group, diethylamino group, dipropylamino group, diisopropylamino group, dibutylamino group, diisobutylamino group, di(sec-butyl)amino group, di(fert-butyl)amino group, dipentylamino group, diisopentylamino group, di(te / Y-pentyl)amino group, dihexylamino group, A / -ethyl-A / -methylamino group, A / -methyl- / V-propylamino group, / V-ethyl-A / -propylamino group and the like.

[0058] The term “carboxylic acid” as used herein is represented by the formula — C(O)OH.

[0059] The term “ester” as used herein is represented by the formula — OC(O)A1or — C(O)OA1, where A1can be alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein.

[0060] The term “ether” as used herein is represented by the formula A1OA2, where A1and A2can be, independently, an alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group described herein.

[0061] The terms “halo,” “halogen” or “halide,” as used herein can be used interchangeably and refer to F, Cl, Br, or I.

[0062] The terms “pseudohalide,” “pseudohalogen” or “pseudohalo,” as used herein can be used interchangeably and refer to functional groups that behave substantially similar to halides. Such functional groups include, by way of example, cyano, thiocyanato, azido, trifluoromethyl, trifluoromethoxy, perfluoroalkyl, and perfluoroalkoxy groups.

[0063] The term “heteroalkyl” as used herein refers to an alkyl group containing at least one heteroatom. Suitable heteroatoms include, but are not limited to, O, N, Si, P and S, wherein the nitrogen, phosphorous and sulfur atoms are optionally oxidized, and the nitrogen heteroatom is optionally quaternized. Heteroalkyls can be substituted as defined above for alkyl groups.ATTORNEY DOCKET NO. 320903-2580

[0064] The term “heteroaryl” as used herein refers to an aromatic group that has at least one heteroatom incorporated within the ring of the aromatic group. Examples of heteroatoms include, but are not limited to, nitrogen, oxygen, sulfur, and phosphorus, where N-oxides, sulfur oxides, and dioxides are permissible heteroatom substitutions. The heteroaryl group can be substituted or unsubstituted. The heteroaryl group can be substituted with one or more groups including, but not limited to, alkyl, aryl, cycloalkyl, alkoxy, amino, ether, halide, hydroxy, nitro, silyl, sulfo-oxo, or thiol as described herein. Heteroaryl groups can be monocyclic, or alternatively fused ring systems. Heteroaryl groups include, but are not limited to, furyl, imidazolyl, pyrimidinyl, tetrazolyl, thienyl, pyridinyl, pyrrolyl, A / -methylpyrrolyl, quinolinyl, isoquinolinyl, pyrazolyl, triazolyl, thiazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiadiazolyl, isothiazolyl, pyridazinyl, pyrazinyl, benzofuranyl, benzodioxolyl, benzothiophenyl, indolyl, indazolyl, benzimidazolyl, imidazopyridinyl, pyrazolopyridinyl, and pyrazolopyrimidinyl. Further not limiting examples of heteroaryl groups include, but are not limited to, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, thiophenyl, pyrazolyl, imidazolyl, benzo[d]oxazolyl, benzo[d]thiazolyl, quinolinyl, quinazolinyl, indazolyl, imidazo[1,2-b]pyridazinyl, imidazo[1,2-a]pyrazinyl, benzo[c][1,2,5]thiadiazolyl, benzo[c][1,2,5]oxadiazolyl, and pyrido[2,3-b]pyrazinyl.

[0065] The terms “heterocycle,” “heterocyclyl,” and “heterocycloalkyl” as used herein can be used interchangeably and refer to single and multi-cyclic aromatic or non-aromatic ring systems in which at least one of the ring members is other than carbon. Thus, the term is inclusive of, but not limited to, “heterocycloalkyl,” “heteroaryl,” “bicyclic heterocycle,” and “polycyclic heterocycle.” Heterocycle includes pyridine, pyrimidine, furan, thiophene, pyrrole, isoxazole, isothiazole, pyrazole, oxazole, thiazole, imidazole, oxazole, including, 1,2,3-oxadiazole, 1,2,5-oxadiazole and 1,3,4-oxadiazole, thiadiazole, including, 1,2,3-thiadiazole, 1,2,5-thiadiazole, and 1,3,4-thiadiazole, triazole, including, 1,2,3-triazole, 1,3,4-triazole, tetrazole, including 1,2,3,4-tetrazole and 1,2,4,5-tetrazole, pyridazine, pyrazine, triazine, including 1,2,4-triazine and 1,3,5-triazine, tetrazine, including 1,2,4,5-tetrazine, pyrrolidine, piperidine, piperazine, morpholine, azetidine, tetrahydropyran, tetra hydrofuran, dioxane, and the like. The term heterocyclyl group can also be a C2 heterocyclyl, C2-C3 heterocyclyl, C2-C4 heterocyclyl, C2-C5 heterocyclyl, C2-C6 heterocyclyl, C2-C7 heterocyclyl, C2-C8 heterocyclyl, C2-C9 heterocyclyl, C2-C10 heterocyclyl, C2-C11 heterocyclyl, and the like up to and including a C2-C18 heterocyclyl. For example, a C2 heterocyclyl comprises a group which has two carbon atoms and at least one heteroatom, including, but not limited to, aziridinyl, diazetidinyl, dihydrodiazetyl, oxiranyl, thiiranyl, and the like. Alternatively, for example, a C5 heterocyclyl comprises a group which has five carbon atoms andATTORNEY DOCKET NO. 320903-2580at least one heteroatom, including, but not limited to, piperidinyl, tetrahydropyranyl, tetrahydrothiopyranyl, diazepanyl, pyridinyl, and the like. It is understood that a heterocyclyl group may be bound either through a heteroatom in the ring, where chemically possible, or one of carbons comprising the heterocyclyl ring.

[0066] The term “bicyclic heterocycle’’ or “bicyclic heterocyclyl” as used herein refers to a ring system in which at least one of the ring members is other than carbon. Bicyclic heterocyclyl encompasses ring systems wherein an aromatic ring is fused with another aromatic ring, or wherein an aromatic ring is fused with a non-aromatic ring. Bicyclic heterocyclyl encompasses ring systems wherein a benzene ring is fused to a 5- or a 6-membered ring containing 1, 2 or 3 ring heteroatoms or wherein a pyridine ring is fused to a 5- or a 6-membered ring containing 1, 2 or 3 ring heteroatoms. Bicyclic heterocyclic groups include, but are not limited to, indolyl, indazolyl, pyrazolo[1,5-a]pyridinyl, benzofuranyl, quinolinyl, quinoxalinyl, 1,3-benzodioxolyl, 2,3-dihydro-1,4-benzodioxinyl, 3,4-dihydro-2H-chromenyl, 1H-pyrazolo[4,3-c]pyridin-3-yl; 1H-pyrrolo[3,2-b]pyridin-3-yl; and 1H-pyrazolo[3,2-b]pyridin-3-yl.

[0067] The term “heterocycloalkyl” or “heterocycloalkylene” as used herein refers to an aliphatic, partially unsaturated or fully saturated, 3- to 14-membered ring system, including single rings of 3 to 8 atoms and bi- and tricyclic ring systems. The heterocycloalkyl ring-systems include one to four heteroatoms independently selected from oxygen, nitrogen, and sulfur, wherein a nitrogen and sulfur heteroatom optionally can be oxidized and a nitrogen heteroatom optionally can be substituted. Representative heterocycloalkyl groups include, but are not limited to, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, and tetrahydrofuryl. The heterocycloalkyl group can be substituted with one or more groups including, but not limited to, alkyl, aryl, heteroaryl, cycloalkyl, alkoxy, amino, ether, halide, hydroxy, nitro, silyl, sulfo-oxo, or thiol as described herein.

[0068] The term “hydroxyl” or “hydroxy” as used herein is represented by the formula — OH.

[0069] The term “ketone” as used herein is represented by the formula A1C(O)A2, where A1and A2can be, independently, an alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein.

[0070] The term “azide” or “azido” as used herein is represented by the formula — N3.

[0071] The term “nitro” as used herein is represented by the formula — NO2.ATTORNEY DOCKET NO. 320903-2580

[0072] The term “nitrile” or “cyano” as used herein is represented by the formula — CN.

[0073] The term “silyl” as used herein is represented by the formula — SiA1A2A3, where A1, A2, and A3can be, independently, hydrogen or an alkyl, cycloalkyl, alkoxy, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein.

[0074] The term “sulfo-oxo” as used herein is represented by the formulas — S(O)A1, — S(O)2A1, — OS(O)2A1, or — OS(O)2OA1, where A1can be hydrogen or an alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein. Throughout this specification “S(O)” is a shorthand notation for S=O. The term “sulfonyl” is used herein to refer to the sulfo-oxo group represented by the formula — S(O)2A1, where A1can be hydrogen or an alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein. The term “sulfone” as used herein is represented by the formula A1S(O)2A2, where A1and A2can be, independently, an alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein. The term “sulfoxide” as used herein is represented by the formula A1S(O)A2, where A1and A2can be, independently, an alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, aryl, or heteroaryl group as described herein.

[0075] The term “thiol” as used herein is represented by the formula -SH.

[0076] The term “thioalkyl" as used herein is represented by the formula -SR where R is a substituted or unsubstituted alkyl group as defined herein.

[0077] “R1,” “R2,” “R3,”... “Rn,” where n is an integer, as used herein can, independently, possess one or more of the groups listed above. For example, if R1is a straight chain alkyl group, one of the hydrogen atoms of the alkyl group can optionally be substituted with a hydroxyl group, an alkoxy group, an alkyl group, a halide, and the like. Depending upon the groups that are selected, a first group can be incorporated within second group or, alternatively, the first group can be pendant ( / .e., attached) to the second group. For example, with the phrase “an alkyl group comprising an amino group,” the amino group can be incorporated within the backbone of the alkyl group. Alternatively, the amino group can be attached to the backbone of the alkyl group. The nature of the group(s) that is (are) selected will determine if the first group is embedded or attached to the second group.

[0078] As described herein, compounds of the invention may contain “optionally substituted” moieties. In general, the term “substituted,” whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitableATTORNEY DOCKET NO. 320903-2580substituent. Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds. In is also contemplated that, in certain aspects, unless expressly indicated to the contrary, individual substituents can be further optionally substituted ( / .e., further substituted, or unsubstituted).

[0079] The term “stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain aspects, their recovery, purification, and use for one or more of the purposes disclosed herein.

[0080] Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; -(CH2)o-4R°; -(CH2)o-40R°; -O(CH2)0-4R°, -0-(CH2)O-4C(0)OR°; -(CH2)O-4CH(OR°)2; -(CH2)0-4SRO; -(CH2)0-4Ph, which may be substituted with R°; -(CH2)o-40(CH2)o-iPh which may be substituted with R°; -CH=CHPh, which may be substituted with R°; -(CH2)0-4O(CH2)0-i-pyridyl which may be substituted with R°; -NO2; -CN; -N3; -(CH2)O-4N(R°)2; -(CH2)0-4N(RO)C(O)RO; -N(R°)C(S)R°; -(CH2)O-4N(R°)C(0)NR°2; -N(RO)C(S)NR°2; -(CH2)0-4N(RO)C(O)ORO; -N(R°)N(R°)C(O)R°; -N(R°)N(R°)C(O)NR°2; -N(R°)N(R°)C(O)OR°; -(CH2)0-4C(O)RO; -C(S)R°; -(CH2)O-4C(0)OR°; -(CH2)O-4C(0)SR°; -(CH2)o-4C(0)OSiR03; -(CH2)0-4OC(O)R°; -OC(O)(CH2)0-4SR-, SC(S)SR°; -(CH2)O-4SC(0)R0; -(CH2)0-4C(O)NRO2; -C(S)NRO2; -C(S)SR°; -(CH2)O_4OC(O)NRO2; -C(O)N(OR°)R°; -C(O)C(O)R°; -C(O)CH2C(O)RO; -C(NOR°)R°; -(CH2)O-4SSR°; -(CH2)O-4S(0)2R°; -(CH2)O-4S(0)2OR°; -(CH2)Q_4OS(O)2R°; -S(O)2NRO2; -(CH2)O-4S(O)RO; -N(R°)S(0)2NRO2; -N(R°)S(O)2R°; -N(OR°)R°; -C(NH)NRO2; -P(O)2R°; -P(O)RO2; -OP(O)R°2; -OP(O)(ORO)2; SiR°3; -(C1-4 straight or branched alkylene)O-N(R°)2; or -(C1-4 straight or branched alkylene)C(O)O-N(R°)2, wherein each R° may be substituted as defined below and is independently hydrogen, C1-6 aliphatic, -CH2Ph, -O(CH2)0-iPh, -CH2-(5-6 membered heteroaryl ring), or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R°, taken together with their intervening atom(s), form a 3-12-membered saturated, partially unsaturated, or aryl mono- orATTORNEY DOCKET NO. 320903-2580bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.

[0081] Suitable monovalent substituents on R° (or the ring formed by taking two independent occurrences of R° together with their intervening atoms), are independently halogen, -(CH2)0-2R*, -(haloR*), -(CH2)O-2OH, -(CH2)O-2OR*, -(CH2)0-2CH(OR*)2; -O(haloR’), -CN, -N3, -(CH2)0_2C(O)R*, -(CH2)O-2C(0)OH, -(CH2)O-2C(0)OR’, -(CH2)O-2SR*, -(CH2)O-2SH, -(CH2)O-2NH2, -(CH2)O-2NHR*, -(CH2)O-2NR*2, -NO2, -SiR*3, -OSiR*3, -C(O)SR* -(C1-4 straight or branched alkylene)C(O)OR*, or -SSR* wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently selected from C1-4 aliphatic, -CH2Ph, -O(CH2)0-iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R° include =0 and =S.

[0082] Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: =0, =S, =NNR*2, =NNHC(O)R*, =NNHC(O)OR*, =NNHS(O)2R*, =NR*, =NOR*, -O(C(R*2))2-3O-, or -S(C(R*2))2-3S-, wherein each independent occurrence of R* is selected from hydrogen, Ci_6aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: -O(CR*2)2-3O-, wherein each independent occurrence of R* is selected from hydrogen, C1-6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0083] Suitable substituents on the aliphatic group of R* include halogen, -R*, -(haloR*), -OH, -OR’, -O(haloR’), -CN, -C(O)OH, -C(O)OR*, -NH2, -NHR*, -NR*2, or-NO2, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C1-4 aliphatic, -CH2Ph, -0(CH2)o-iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0084] Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include -Rt, -NRt2, -C(O)Rt, -C(O)ORt, -C(O)C(O)Rt, -C(O)CH2C(O)Rt, -S(O)2R+, -S(O)2NR+2I-C(S)NR+2I-C(NH)NR+2, or -N(R+)S(O)2R+; wherein each Rt isATTORNEY DOCKET NO. 320903-2580independently hydrogen, C1-6 aliphatic which may be substituted as defined below, unsubstituted -OPh, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of Rf, taken together with their intervening atom(s) form an unsubstituted 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0085] Suitable substituents on the aliphatic group of R+ are independently halogen, -R*, -(haloR*), -OH, -OR*, -O(haloR’), -CN, -C(O)OH, -C(O)OR*, -NH2, -NHR*, -NR*2, or — NO2, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C1-4 aliphatic, -CH2Ph, -0(CH2)o-iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0086] The term “leaving group” refers to an atom (or a group of atoms) with electron withdrawing ability that can be displaced as a stable species, taking with it the bonding electrons. Examples of suitable leaving groups include halides and sulfonate esters, including, but not limited to, trifl ate, mesylate, tosylate, and brosylate.

[0087] Compounds described herein can contain one or more double bonds and, thus, potentially give rise to cis / trans (E / Z) isomers, as well as other conformational isomers. Unless stated to the contrary, the invention includes all such possible isomers, as well as mixtures of such isomers.

[0088] Unless stated to the contrary, a formula with chemical bonds shown only as solid lines and not as wedges or dashed lines contemplates each possible isomer, e.g., each enantiomer and diastereomer, and a mixture of isomers, such as a racemic or scalemic mixture. Compounds described herein can contain one or more asymmetric centers and, thus, potentially give rise to diastereomers and optical isomers. Unless stated to the contrary, the present invention includes all such possible diastereomers as well as their racemic mixtures, their substantially pure resolved enantiomers, all possible geometric isomers, and pharmaceutically acceptable salts thereof. Mixtures of stereoisomers, as well as isolated specific stereoisomers, are also included. During the course of the synthetic procedures used to prepare such compounds, or in using racemization or epimerization procedures known to those skilled in the art, the products of such procedures can be a mixture of stereoisomers.

[0089] Many organic compounds exist in optically active forms having the ability to rotate the plane of plane-polarized light. In describing an optically active compound, the prefixes D and L orATTORNEY DOCKET NO. 320903-2580R and S are used to denote the absolute configuration of the molecule about its chiral center(s). The prefixes D and L or (+) and (-) are employed to designate the sign of rotation of plane-polarized light by the compound, with (-) or L meaning that the compound is levorotatory. A compound prefixed with (+) or D is dextrorotatory. For a given chemical structure, these compounds, called stereoisomers, are identical except that they are non-superimposable mirror images of one another. A specific stereoisomer can also be referred to as an enantiomer, and a mixture of such isomers is often called an enantiomeric mixture. A 50:50 mixture of enantiomers is referred to as a racemic mixture. Many of the compounds described herein can have one or more chiral centers and therefore can exist in different enantiomeric forms. If desired, a chiral carbon can be designated with an asterisk (*). When bonds to the chiral carbon are depicted as straight lines in the disclosed formulas, it is understood that both the (R) and (S) configurations of the chiral carbon, and hence both enantiomers and mixtures thereof, are embraced within the formula. As is used in the art, when it is desired to specify the absolute configuration about a chiral carbon, one of the bonds to the chiral carbon can be depicted as a wedge (bonds to atoms above the plane) and the other can be depicted as a series or wedge of short parallel lines is (bonds to atoms below the plane). The Cahn-lngold-Prelog system can be used to assign the (R) or (S) configuration to a chiral carbon.

[0090] The term “substantially R” or “substantially S” with respect to the stereochemistry at a chiral center is defined as an enantiomeric excess of at least 95% and up to 100% of the R or S enantiomer.

[0091] Compounds described herein comprise atoms in both their natural isotopic abundance and in non-natural abundance. The disclosed compounds can be isotopically-labeled or isotopically-substituted compounds identical to those described, but for the fact that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number typically found in nature. Examples of isotopes that can be incorporated into compounds of the invention include isotopes of hydrogen, carbon, nitrogen, oxygen, sulfur, fluorine and chlorine, such as2H,3H,13C,14C,15N,18O,17O,35S,18F, and36CI, respectively. Compounds further comprise prodrugs thereof and pharmaceutically acceptable salts of said compounds or of said prodrugs which contain the aforementioned isotopes and / or other isotopes of other atoms are within the scope of this invention. Certain isotopically-labeled compounds of the present invention, for example those into which radioactive isotopes such as3H and14C are incorporated, are useful in drug and / or substrate tissue distribution assays. Tritiated, i.e.,3H, and carbon-14, i.e.,14C, isotopes are particularly preferred for their ease of preparation andATTORNEY DOCKET NO. 320903-2580detectability. Further, substitution with heavier isotopes such as deuterium, i.e.,2H, can afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements and, hence, may be preferred in some circumstances. I sotopically labeled compounds of the present invention and prodrugs thereof can generally be prepared by carrying out the procedures below, by substituting a readily available isotopically labeled reagent for a non- isotopically labeled reagent.

[0092] The compounds described in the invention can be present as a solvate. In some cases, the solvent used to prepare the solvate is an aqueous solution, and the solvate is then often referred to as a hydrate. The compounds can be present as a hydrate, which can be obtained, for example, by crystallization from a solvent or from aqueous solution. In this connection, one, two, three or any arbitrary number of solvent or water molecules can combine with the compounds according to the invention to form solvates and hydrates. Unless stated to the contrary, the invention includes all such possible solvates.

[0093] It is also appreciated that certain compounds described herein can be present as an equilibrium of tautomers. For example, ketones with an a-hydrogen can exist in an equilibrium of the keto form and the enol form.keto form enol form amide form imidic acid form Likewise, amides with an / V-hydrogen can exist in an equilibrium of the amide form and the imidic acid form. Unless stated to the contrary, the invention includes all such possible tautomers.

[0094] It is known that chemical substances form solids which are present in different states of order which are termed polymorphic forms or modifications. The different modifications of a polymorphic substance can differ greatly in their physical properties. The compounds according to the invention can be present in different polymorphic forms, with it being possible for particular modifications to be metastable. Unless stated to the contrary, the invention includes all such possible polymorphic forms.

[0095] In some aspects, a structure of a compound can be represented by a formula:ATTORNEY DOCKET NO. 320903-2580

[0096] which is understood to be equivalent to a formula:Rn(a)Rn(d)

[0097] wherein n is typically an integer. That is, R" is understood to represent five independent substituents, Rn<a>, Rn<b>, Rn<c>, Rn<d>, and R',(e). By “independent substituents,” it is meant that each R substituent can be independently defined. For example, if in one instance Rn<a> is halogen, then Rn(b)is not necessarily halogen in that instance.

[0098] As used herein, “administering” can refer to an administration that is oral, topical, intravenous, subcutaneous, transcutaneous, transdermal, intramuscular, intra-joint, parenteral, intra-arteriole, intradermal, intraventricular, intraosseous, intraocular, intracranial, intraperitoneal, intralesional, intranasal, intracardiac, intraarticular, intracavernous, intrathecal, intravireal, intracerebral, and intracerebroventricular, intratympanic, intracochlear, rectal, vaginal, by inhalation, by catheters, stents or via an implanted reservoir or other device that administers, either actively or passively (e.g. by diffusion) a composition the perivascular space and adventitia. For example, a medical device such as a stent can contain a composition or formulation disposed on its surface, which can then dissolve or be otherwise distributed to the surrounding tissue and cells. The term “parenteral” can include subcutaneous, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional, and intracranial injections or infusion techniques. Administration can be continuous or intermittent. In various aspects, a preparation can be administered therapeutically; that is, administered to treat an existing disease or condition. In further various aspects, a preparation can be administered prophylactically; that is, administered for prevention of a disease or condition.

[0099] As used interchangeably herein, “subject,” “individual,” or “patient” can refer to a vertebrate organism, such as a mammal (e.g., human). " Subject" can also refer to a cell, a population of cells, a tissue, an organ, or an organism, preferably to human and constituents thereof.

[0100] As used herein, the terms "treating" and "treatment" can refer generally to obtaining a desired pharmacological and / or physiological effect. The effect can be, but does not necessarily have to be, prophylactic in terms of preventing or partially preventing a disease, symptom, or condition thereof, such as, for example, cancer or one or more symptoms associated therewith.ATTORNEY DOCKET NO. 320903-2580The effect can be therapeutic in terms of a partial or complete cure of a disease, condition, symptom or adverse effect attributed to the disease, disorder, or condition. The term "treatment" as used herein can include any treatment of cancer or other parasitic infection in a subject, particularly a human and can include any one or more of the following: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., mitigating or ameliorating the disease and / or its symptoms or conditions. The term "treatment" as used herein can refer to both therapeutic treatment alone, prophylactic treatment alone, or both therapeutic and prophylactic treatment. Those in need of treatment (subjects in need thereof) can include those already with the disorder and / or those in which the disorder is to be prevented. As used herein, the term "treating", can include inhibiting the disease, disorder or condition, e.g., impeding its progress; and relieving the disease, disorder, or condition, e.g., causing regression of the disease, disorder and / or condition. Treating the disease, disorder, or condition can include ameliorating at least one symptom of the particular disease, disorder, or condition, even if the underlying pathophysiology is not affected, e.g., such as treating the pain of a subject by administration of an analgesic agent even though such agent does not treat the cause of the pain.

[0101] As used herein, the term “prevent” or “preventing” refers to precluding, averting, obviating, forestalling, stopping, or hindering something from happening, especially by advance action. It is understood that where reduce, inhibit, or prevent are used herein, unless specifically indicated otherwise, the use of the other two words is also expressly disclosed.

[0102] As used herein, “therapeutic” can refer to treating, healing, and / or ameliorating a disease, disorder, condition, or side effect, or to decreasing in the rate of advancement of a disease, disorder, condition, or side effect.

[0103] As used herein, “effective amount” can refer to the amount of a disclosed compound or pharmaceutical composition provided herein that is sufficient to effect beneficial or desired biological, emotional, medical, or clinical response of a cell, tissue, system, animal, or human. An effective amount can be administered in one or more administrations, applications, or dosages. The term can also include within its scope amounts effective to enhance or restore to substantially normal physiological function.

[0104] For example, it is well within the skill of the art to start doses of a compound at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosageATTORNEY DOCKET NO. 320903-2580until the desired effect is achieved. If desired, the effective daily dose can be divided into multiple doses for purposes of administration. Consequently, single dose compositions can contain such amounts or submultiples thereof to make up the daily dose. The dosage can be adjusted by the individual physician in the event of any contraindications. It is generally preferred that a maximum dose of the pharmacological agents of the invention (alone or in combination with other therapeutic agents) be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.

[0105] A response to a therapeutically effective dose of a disclosed compound and / or pharmaceutical composition, for example, can be measured by determining the physiological effects of the treatment or medication, such as the decrease or lack of disease symptoms following administration of the treatment or pharmacological agent. Other assays will be known to one of ordinary skill in the art and can be employed for measuring the level of the response. The amount of a treatment may be varied for example by increasing or decreasing the amount of a disclosed compound and / or pharmaceutical composition, by changing the disclosed compound and / or pharmaceutical composition administered, by changing the route of administration, by changing the dosage timing and so on. Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products.

[0106] As used herein, the term “prophylactically effective amount” refers to an amount effective for preventing onset or initiation of a disease or condition.

[0107] The term “pharmaceutically acceptable” describes a material that is not biologically or otherwise undesirable, / .e., without causing an unacceptable level of undesirable biological effects or interacting in a deleterious manner.

[0108] The term “pharmaceutically acceptable salts”, as used herein, means salts of the active principal agents which are prepared with acids or bases that are tolerated by a biological system or tolerated by a subject or tolerated by a biological system and tolerated by a subject when administered in a therapeutically effective amount. When compounds of the present disclosure contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable base addition salts include, butATTORNEY DOCKET NO. 320903-2580are not limited to, sodium, potassium, calcium, ammonium, organic amino, magnesium salt, lithium salt, strontium salt or a similar salt. When compounds of the present disclosure contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable acid addition salts include, but are not limited to; those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like.

[0109] The term “pharmaceutically acceptable prodrug” or “prodrug” represents those prodrugs of the compounds of the present disclosure which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit / risk ratio, and effective for their intended use. Prodrugs of the present disclosure can be rapidly transformed in vivo to a parent compound having a structure of a disclosed compound, for example, by hydrolysis in blood. A thorough discussion is provided in T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, V. 14 of the A. C. S. Symposium Series, and in Edward B. Roche, ed., Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press (1987).

[0110] As used herein, “dose,” “unit dose,” or “dosage” can refer to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of a disclosed compound and / or a pharmaceutical composition thereof calculated to produce the desired response or responses in association with its administration.

[0111] Certain materials, compounds, compositions, and components disclosed herein can be obtained commercially or readily synthesized using techniques generally known to those of skill in the art. For example, the starting materials and reagents used in preparing the disclosed compounds and compositions are either available from commercial suppliers such as Aldrich Chemical Co., (Milwaukee, Wis.), Acros Organics (Morris Plains, N. J ), Fisher Scientific (Pittsburgh, Pa.), or Sigma (St. Louis, Mo.) or are prepared by methods known to those skilled inATTORNEY DOCKET NO. 320903-2580the art following procedures set forth in references such as Fieser and Fieser’s Reagents for Organic Synthesis, Volumes 1-17 (John Wiley and Sons, 1991); Rodd’s Chemistry of Carbon Compounds, Volumes 1-5 and Supplemental (Elsevier Science Publishers, 1989); Organic Reactions, Volumes 1-40 (John Wiley and Sons, 1991); March’s Advanced Organic Chemistry, (John Wiley and Sons, 4th Edition); and Larock’s Comprehensive Organic Transformations (VCH Publishers Inc., 1989).

[0112] Unless otherwise expressly stated, it is in no way intended that any method set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not actually recite an order to be followed by its steps or it is not otherwise specifically stated in the claims or descriptions that the steps are to be limited to a specific order, it is no way intended that an order be inferred, in any respect. This holds for any possible nonexpress basis for interpretation, including: matters of logic with respect to arrangement of steps or operational flow; plain meaning derived from grammatical organization or punctuation; and the number or type of embodiments described in the specification.

[0113] Disclosed are the components to be used to prepare the compositions of the invention as well as the compositions themselves to be used within the methods disclosed herein. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutation of these compounds cannot be explicitly disclosed, each is specifically contemplated and described herein. For example, if a particular compound is disclosed and discussed and a number of modifications that can be made to a number of molecules including the compounds are discussed, specifically contemplated is each and every combination and permutation of the compound and the modifications that are possible unless specifically indicated to the contrary. Thus, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited each is individually and collectively contemplated meaning combinations, A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are considered disclosed. Likewise, any subset or combination of these is also disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E would be considered disclosed. This concept applies to all aspects of this application including, but not limited to, steps in methods of making and using the compositions of the invention. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the methods of the invention.ATTORNEY DOCKET NO. 320903-2580

[0114] It is understood that the compositions disclosed herein have certain functions. Disclosed herein are certain structural requirements for performing the disclosed functions, and it is understood that there are a variety of structures that can perform the same function that are related to the disclosed structures, and that these structures will typically achieve the same result.

[0115] As used herein, the terms “optional” or “optionally” means that the subsequently described event or circumstance can or cannot occur, and that the description includes instances where said event or circumstance occurs and instances where it does not.

[0116] Unless otherwise specified, temperatures referred to herein are based on atmospheric pressure ( / .e. one atmosphere).PKD1 Inhibitors and Methods for Making and Using Thereof

[0117] PKD1 Inhibitors

[0118] Described herein are compounds and methods for treating cancer in a subject. In one aspect, a compound having a formula represented by structure I or the pharmaceutically acceptable salt thereof can be used in the methods described hereinwherein- represents a single or double bond;Y is C or NR3, wherein R3is absent, hydrogen, or an alkyl group;Z is C or N;R1and R2together with the atoms to which they are attached form an aryl ring, a heteroaryl ring, a cycloalkyl ring, or heterocycloalkyl ring, orR1and R2are independently (i) a substituted alkyl group or an unsubstituted alkyl group; (ii) a substituted alkenyl group or an unsubstituted alkenyl group; (iii) a thioalkyl group; (iv) an aminoalkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substitutedATTORNEY DOCKET NO. 320903-2580heteroaryl group or an unsubstituted heteroaryl group; (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group, provided that R1 and R2are not both H; andwhereinR4and R5are, independently, (i) a haloalkyl group (ii) hydrogen, (iii) a substituted heteroaryl group or an unsubstituted heteroaryl group; (iv) a substituted alkyl group or an unsubstituted alkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted alkenyl group or an unsubstituted alkenyl group; (vii) a substituted cycloalkyl group or an unsubstituted cycloalkyl group; or (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group;the stereochemistry at a is racemic, substantially R, or substantially S;the stereochemistry at b is racemic, substantially R, or substantially S; andthe stereochemistry at c is racemic, substantially R, or substantially S.

[0119] In one aspect, Z in structure I is C. In one aspect, Y in structure I is C. In one aspect, - in structure I represents a single bond. In another aspect, Ri and R2 in structure I together with the atoms to which they are attached form a heterocycloalkyl ring, wherein the heterocycloalkyl ring is optionally fused with a (i) a substituted heteroaryl group or an unsubstituted heteroaryl group or (ii) a substituted aryl group or an unsubstituted aryl group.

[0120] In one aspect, X in structure I is -CH2OH orATTORNEY DOCKET NO. 320903-2580wherein R4is haloalkyl.

[0121] In one aspect, the compound is one of the following structures(R6)nwhereinn is an integer from 1 to 4; andeach R6is independently selected from hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; or■9■8bwherein R7and R9are C1-C6 alkyl, R8is hydroxy or alkoxy, and R4is haloalkyl; orATTORNEY DOCKET NO. 320903-2580(Rio)nIVwhereinn is an integer from 1 to 4; andR4and each R is independently selected from hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orVwhereinR10 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orATTORNEY DOCKET NO. 320903-2580whereinR11 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orwhereinR11 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted alkenyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orATTORNEY DOCKET NO. 320903-2580RnNHR4VIIIwhereinR11 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted alkenyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group.

[0122] In one aspect, when the compound has the formula II, each of R6is hydrogen. In one aspect, when the compound has the formula II, n is 3, wherein a first R6is hydroxy and a second and third R6is a C1-C6 alkyl group. In one aspect, when the compound has the formula II, X is -CH2OH orwherein R4 is haloalkyl. In one aspect, when the compound has the formula II, R4 is a C1 to C5 perhalogenated alkyl group such as, for example, CF3 or CCl3.

[0123] In one aspect, when the compound has the formula III, R7 and R9 are each tert-butyl and Rs is hydroxy. In one aspect, when the compound has the formula III, R4 is CCI3. In one aspect, when the compound has the formula III, the stereochemistry at carbon b is substantially R or S.

[0124] In one aspect, when the compound has the formula VI, VII, or VIII, R4is a substituted or unsubstituted aryl group or a substituted or unsubstituted heteroaryl group and Rn is hydrogen or a substituted or unsubstituted aryl group or a substituted or unsubstituted heteroaryl group.ATTORNEY DOCKET NO. 320903-2580

[0125] In one aspect, the compound has one of the following structureswhereinR2is (i) a substituted alkyl group or an unsubstituted alkyl group; (ii) a substituted alkenyl group or an unsubstituted alkenyl group; (iii) a thioalkyl group; (iv) an aminoalkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted heteroaryl group or an unsubstituted heteroaryl group; or (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group;the stereochemistry at a is racemic, substantially R, or substantially S;the stereochemistry at b is racemic, substantially R, or substantially S; andR4is haloalkyl; orb■2whereinR1and R2together with the atoms to which they are attached form an aryl ring, a heteroaryl ring, a cycloalkyl ring, or heterocycloalkyl ring;the stereochemistry at b is racemic, substantially R, or substantially S; andR4is haloalkyl; orATTORNEY DOCKET NO. 320903-2580whereinZ is CH, N, or NH+;Ri is (i) a substituted alkyl group or an unsubstituted alkyl group; (ii) a substituted alkenyl group or an unsubstituted alkenyl group; (iii) a thioalkyl group; (iv) an aminoalkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted heteroaryl group or an unsubstituted heteroaryl group; (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group;R4is haloalkyl;the stereochemistry at b is racemic, substantially R, or substantially S; andthe stereochemistry at c is racemic, substantially R, or substantially S.

[0126] In one aspect, the compounds described herein can be prepared as a racemic mixture initially then subsequently the enantiomers can be separated using chiral HPLC / SFC to isolate each enantiomer.

[0127] In one aspect, the compound is one of the following compounds:ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580

[0128] In one aspect, the compound is one of the following compounds:ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580ATTORNEY DOCKET NO. 320903-2580or

[0129] In one aspect, the compounds of structure I can be synthesized using the exemplary synthetic procedures provided in the Examples and FIGS. 1A-1J, 2A-2Z, and 3A-3J.

[0130] Methods for Treating Cancer

[0131] Understanding tumor metabolism is important in cancer progression, as it offers critical insights into its aggressive behavior and presents significant potential for therapeutic intervention. For example, glioblastoma multiforme (GBM) cells exhibit extensive metabolic reprogramming, characterized by a shift towards aerobic glycolysis and increased glutaminolysis, which support their rapid proliferation and survival [11-13], This metabolic plasticity is intrinsically linked to the GBM's aggressive nature, contributing to its rapid growth, invasion, and resistance to conventional therapies, influencing tumor heterogeneity

[0014] ,

[0132] A metabolic target for the treatment of GBM is pyruvate dehydrogenase kinase 1 (PDK1), an enzyme that regulates the conversion of pyruvate into acetyl-CoA, directing cellular metabolism towards aerobic respiration. Elevated levels of PDK1 in GBM have been associated with promoting a shift towards glycolysis, contributing to GBM growth [15-17], The targeting of PDK1 reversed this metabolic adaptation, particularly through sodium dichloroacetate (DCA), a small molecule inhibitor that inhibits PDK1, promoting oxidative phosphorylation (OXPHOS) and reducing reliance on glycolysis [15, 18, 19],

[0133] DCA treatment effectively reduced epidermal growth factor receptor (EGFR) levels in both GBM and recurrent models of GBM, in vitro and in vivo [19, 20, 3, 21], DCA's ability to modulate metabolic pathways made it a candidate, and it was used across various cancers, includingATTORNEY DOCKET NO. 320903-2580breast, gastric, renal, melanoma, colon cancers, and leukemia [22-26], Further, DCA is currently used in clinical trials for GBM (ClinicalTrials.gov ID # NCT01111097). Despite its promise, DCA is limited by side effects such as neurotoxicity and individual variability in response, highlighting the urgent need for the development of novel small molecule inhibitors that could provide more effective and safer therapeutic options. Advancing the treatment landscape for GBM with these inhibitors is vital, as it could lead to improved patient outcomes by specifically tackling the metabolic vulnerabilities of GBM cells.

[0134] In one aspect, disclosed herein is a method for the treatment or prevention of cancer in a subject, the method including the step of administering to the subject an effective amount of at least one disclosed compound, or a pharmaceutically acceptable salt thereof, or the disclosed pharmaceutical composition. As demonstrated herein, the PDK1 inhibitors decreased expression of PDK1 and phosphorylated EGFR (pEGFR), key oncogenic markers in GBM. The PDK1 inhibitors significantly reduced cell viability, induced G2 / M cell cycle arrest, inhibited glycolysis, and promoted oxidative phosphorylation. The PDK1 inhibitors effectively suppressed U87 cell migration and invasion compared to dichloroacetate (DCA), another PDK1 inhibitor. Furthermore, treatment with the inhibitors increased reactive oxygen species (ROS) production and decreased lactate release, indicating a shift from glycolysis to oxidative metabolism. Treatment using the PDK1 inhibitors described herein can prolong survival, delayed tumor-associated weight loss, and reduced tumor burden.

[0135] The cancer is associated with an elevated level of pyruvate dehydrogenase kinase 1 (PDK1) in the subject, which includes glioblastoma, medulloblastoma, or breast cancer (e.g., triple negative breast cancers). In some aspects, the subject is a human. In another aspect, the subject has been diagnosed with a need for treatment of cancer prior to the administering step.

[0136] In one aspect, the compounds described herein are administered orally to the subject. In another aspect, the compound is administered intravenously or intramuscularly to the subject. In one aspect, the compound is administered at a dosage of from about 50 mg per day to about 1,000 mg per day, or about 50 mg per day, 50 mg per day, 100 mg per day, 150 mg per day, 200 mg per day, 250 mg per day, 300 mg per day, 350 mg per day, 400 mg per day, 450 mg per day, 500 mg per day, 550 mg per day, 600 mg per day, 650 mg per day, 700 mg per day, 750 mg per day, 800 mg per day, 850 mg per day, 900 mg per day, 950 mg per day, or 1,000 mg per day, where any value can be a lower and upper endpoint of a range (e.g., 100 mg per day to 300 mg per day).ATTORNEY DOCKET NO. 320903-2580

[0137] Pharmaceutical Compositions

[0138] In various aspects, the present disclosure relates to pharmaceutical compositions comprising a therapeutically effective amount of at least one disclosed compound, at least one product of a disclosed method, or a pharmaceutically acceptable salt thereof. As used herein, “pharmaceutically-acceptable carriers” means one or more of a pharmaceutically acceptable diluents, preservatives, antioxidants, solubilizers, emulsifiers, coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, and adjuvants. The disclosed pharmaceutical compositions can be conveniently presented in unit dosage form and prepared by any of the methods well known in the art of pharmacy and pharmaceutical sciences.

[0139] In a further aspect, the disclosed pharmaceutical compositions comprise a therapeutically effective amount of at least one disclosed compound, at least one product of a disclosed method, or a pharmaceutically acceptable salt thereof as an active ingredient, a pharmaceutically acceptable carrier, optionally one or more other therapeutic agent, and optionally one or more adjuvant. The disclosed pharmaceutical compositions include those suitable for oral, rectal, topical, pulmonary, nasal, and parenteral administration, although the most suitable route in any given case will depend on the particular host, and nature and severity of the conditions for which the active ingredient is being administered. In a further aspect, the disclosed pharmaceutical composition can be formulated to allow administration orally, nasally, via inhalation, parenterally, paracancerally, transmucosally, transdemnally, intramuscularly, intravenously, intradermally, subcutaneously, intraperitoneally, intraventricularly, intracranially and intratumorally.

[0140] As used herein, “parenteral administration” includes administration by bolus injection or infusion, as well as administration by intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular subarachnoid, intraspinal, epidural and intrasternal injection and infusion.

[0141] In various aspects, the present disclosure also relates to a pharmaceutical composition comprising a pharmaceutically acceptable carrier or diluent and, as active ingredient, a therapeutically effective amount of a disclosed compound, a product of a disclosed method of making, a pharmaceutically acceptable salt, a hydrate thereof, a solvate thereof, a polymorph thereof, or a stereochemically isomeric form thereof. In a further aspect, a disclosed compound, a product of a disclosed method of making, a pharmaceutically acceptable salt, a hydrate thereof, a solvate thereof, a polymorph thereof, or a stereochemically isomeric form thereof, or anyATTORNEY DOCKET NO. 320903-2580subgroup or combination thereof may be formulated into various pharmaceutical forms for administration purposes.

[0142] In practice, the compounds of the present disclosure, or pharmaceutically acceptable salts thereof, of the present disclosure can be combined as the active ingredient in intimate admixture with a pharmaceutical carrier according to conventional pharmaceutical compounding techniques. The carrier can take a wide variety of forms depending on the form of preparation desired for administration, e.g., oral or parenteral (including intravenous). Thus, the pharmaceutical compositions of the present disclosure can be presented as discrete units suitable for oral administration such as capsules, cachets or tablets each containing a predetermined amount of the active ingredient. Further, the compositions can be presented as a powder, as granules, as a solution, as a suspension in an aqueous liquid, as a non-aqueous liquid, as an oil-in-water emulsion or as a water-in-oil liquid emulsion. In addition to the common dosage forms set out above, the compounds of the present disclosure, and / or pharmaceutically acceptable salt(s) thereof, can also be administered by controlled release means and / or delivery devices. The compositions can be prepared by any of the methods of pharmacy. In general, such methods include a step of bringing into association the active ingredient with the carrier that constitutes one or more necessary ingredients. In general, the compositions are prepared by uniformly and intimately admixing the active ingredient with liquid carriers or finely divided solid carriers or both. The product can then be conveniently shaped into the desired presentation.

[0143] It is especially advantageous to formulate the aforementioned pharmaceutical compositions in unit dosage form for ease of administration and uniformity of dosage. The term “unit dosage form,” as used herein, refers to physically discrete units suitable as unitary dosages, each unit containing a predetermined quantity of active ingredient calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. That is, a “unit dosage form” is taken to mean a single dose wherein all active and inactive ingredients are combined in a suitable system, such that the patient or person administering the drug to the patient can open a single container or package with the entire dose contained therein and does not have to mix any components together from two or more containers or packages. Typical examples of unit dosage forms are tablets (including scored or coated tablets), capsules or pills for oral administration; single dose vials for injectable solutions or suspension; suppositories for rectal administration; powder packets; wafers; and segregated multiples thereof. This list of unit dosage forms is not intended to be limiting in any way, but merely to represent typical examples of unit dosage forms.ATTORNEY DOCKET NO. 320903-2580

[0144] The pharmaceutical compositions disclosed herein comprise a compound of the present disclosure (or pharmaceutically acceptable salts thereof) as an active ingredient, a pharmaceutically acceptable carrier, and optionally one or more additional therapeutic agents. In various aspects, the disclosed pharmaceutical compositions can include a pharmaceutically acceptable carrier and a disclosed compound, or a pharmaceutically acceptable salt thereof. In a further aspect, a disclosed compound, or pharmaceutically acceptable salt thereof, can also be included in a pharmaceutical composition in combination with one or more other therapeutically active compounds. The instant compositions include compositions suitable for oral, rectal, topical, and parenteral (including subcutaneous, intramuscular, and intravenous) administration, although the most suitable route in any given case will depend on the particular host, and nature and severity of the conditions for which the active ingredient is being administered. The pharmaceutical compositions can be conveniently presented in unit dosage form and prepared by any of the methods well known in the art of pharmacy.

[0145] Techniques and compositions for making dosage forms useful for materials and methods described herein are described, for example, in the following references: Modern Pharmaceutics, Chapters 9 and 10 (Banker & Rhodes, Editors, 1979); Pharmaceutical Dosage Forms: Tablets (Lieberman et al., 1981); Ansel, Introduction to Pharmaceutical Dosage Forms 2nd Edition (1976); Remington's Pharmaceutical Sciences, 17th ed. (Mack Publishing Company, Easton, Pa., 1985); Advances in Pharmaceutical Sciences (David Ganderton, Trevor Jones, Eds., 1992); Advances in Pharmaceutical Sciences Vol 7. (David Ganderton, Trevor Jones, James McGinity, Eds., 1995); Aqueous Polymeric Coatings for Pharmaceutical Dosage Forms (Drugs and the Pharmaceutical Sciences, Series 36 (James McGinity, Ed., 1989); Pharmaceutical Particulate Carriers: Therapeutic Applications: Drugs and the Pharmaceutical Sciences, Vol 61 (Alain Rolland, Ed., 1993); Drug Delivery to the Gastrointestinal Tract (Ellis Horwood Books in the Biological Sciences. Series in Pharmaceutical Technology; J. G. Hardy, S. S. Davis, Clive G. Wilson, Eds.); Modern Pharmaceutics Drugs and the Pharmaceutical Sciences, Vol 40 (Gilbert S. Banker, Christopher T. Rhodes, Eds.).

[0146] The compounds described herein are typically to be administered in admixture with suitable pharmaceutical diluents, excipients, extenders, or carriers (termed herein as a pharmaceutically acceptable carrier, or a carrier) suitably selected with respect to the intended form of administration and as consistent with conventional pharmaceutical practices. The deliverable compound will be in a form suitable for oral, rectal, topical, intravenous injection or parenteral administration. Carriers include solids or liquids, and the type of carrier is chosen basedATTORNEY DOCKET NO.320903-2580on the type of administration being used. The compounds may be administered as a dosage that has a known quantity of the compound.

[0147] Because of the ease in administration, oral administration can be a preferred dosage form, and tablets and capsules represent the most advantageous oral dosage unit forms in which case solid pharmaceutical carriers are obviously employed. However, other dosage forms may be suitable depending upon clinical population (e.g., age and severity of clinical condition), solubility properties of the specific disclosed compound used, and the like. Accordingly, the disclosed compounds can be used in oral dosage forms such as pills, powders, granules, elixirs, tinctures, suspensions, syrups, and emulsions. In preparing the compositions for oral dosage form, any convenient pharmaceutical media can be employed. For example, water, glycols, oils, alcohols, flavoring agents, preservatives, coloring agents and the like can be used to form oral liquid preparations such as suspensions, elixirs and solutions; while carriers such as starches, sugars, microcrystalline cellulose, diluents, granulating agents, lubricants, binders, disintegrating agents, and the like can be used to form oral solid preparations such as powders, capsules and tablets. Because of their ease of administration, tablets and capsules are the preferred oral dosage units whereby solid pharmaceutical carriers are employed. Optionally, tablets can be coated by standard aqueous or nonaqueous techniques.

[0148] The disclosed pharmaceutical compositions in an oral dosage form can comprise one or more pharmaceutical excipient and / or additive. Non-limiting examples of suitable excipients and additives include gelatin, natural sugars such as raw sugar or lactose, lecithin, pectin, starches (for example corn starch or amylose), dextran, polyvinyl pyrrolidone, polyvinyl acetate, gum arabic, alginic acid, tylose, talcum, lycopodium, silica gel (for example colloidal), cellulose, cellulose derivatives (for example cellulose ethers in which the cellulose hydroxy groups are partially etherified with lower saturated aliphatic alcohols and / or lower saturated, aliphatic oxyalcohols, for example methyl oxypropyl cellulose, methyl cellulose, hydroxypropyl methyl cellulose, hydroxypropyl methyl cellulose phthalate), fatty acids as well as magnesium, calcium or aluminum salts of fatty acids with 12 to 22 carbon atoms, in particular saturated (for example stearates), emulsifiers, oils and fats, in particular vegetable (for example, peanut oil, castor oil, olive oil, sesame oil, cottonseed oil, corn oil, wheat germ oil, sunflower seed oil, cod liver oil, in each case also optionally hydrated); glycerol esters and polyglycerol esters of saturated fatty acids C12H24O2 to C18H36O2 and their mixtures, it being possible for the glycerol hydroxy groups to be totally or also only partly esterified (for example mono-, di- and triglycerides); pharmaceutically acceptable mono- or multivalent alcohols and polyglycols such as polyethyleneATTORNEY DOCKET NO. 320903-2580glycol and derivatives thereof, esters of aliphatic saturated or unsaturated fatty acids (2 to 22 carbon atoms, in particular 10-18 carbon atoms) with monovalent aliphatic alcohols (1 to 20 carbon atoms) or multivalent alcohols such as glycols, glycerol, diethylene glycol, pentacrythritol, sorbitol, mannitol and the like, which may optionally also be etherified, esters of citric acid with primary alcohols, acetic acid, urea, benzyl benzoate, dioxolanes, glyceroformals, tetra hydrofurfuryl alcohol, polyglycol ethers with C1-C12-alcohols, dimethylacetamide, lactamides, lactates, ethyl carbonates, silicones (in particular medium-viscous polydimethyl siloxanes), calcium carbonate, sodium carbonate, calcium phosphate, sodium phosphate, magnesium carbonate and the like.

[0149] Other auxiliary substances useful in preparing an oral dosage form are those which cause disintegration (so-called disintegrants), such as: cross-linked polyvinyl pyrrolidone, sodium carboxymethyl starch, sodium carboxymethyl cellulose or microcrystalline cellulose. Conventional coating substances may also be used to produce the oral dosage form. Those that may for example be considered are: polymerizates as well as copolymerizates of acrylic acid and / or methacrylic acid and / or their esters; copolymerizates of acrylic and methacrylic acid esters with a lower ammonium group content (for example EudragitR RS), copolymerizates of acrylic and methacrylic acid esters and trimethyl ammonium methacrylate (for example EudragitR RL); polyvinyl acetate; fats, oils, waxes, fatty alcohols; hydroxypropyl methyl cellulose phthalate or acetate succinate; cellulose acetate phthalate, starch acetate phthalate as well as polyvinyl acetate phthalate, carboxy methyl cellulose; methyl cellulose phthalate, methyl cellulose succinate, -phthalate succinate as well as methyl cellulose phthalic acid half ester; zein; ethyl cellulose as well as ethyl cellulose succinate; shellac, gluten; ethylcarboxyethyl cellulose; ethacrylate-maleic acid anhydride copolymer; maleic acid anhydride-vinyl methyl ether copolymer; styrol-maleic acid copolymerizate; 2-ethyl-hexyl-acrylate maleic acid anhydride; crotonic acid-vinyl acetate copolymer; glutaminic acid / glutamic acid ester copolymer; carboxymethylethylcellulose glycerol monooctanoate; cellulose acetate succinate; polyarginine.

[0150] Plasticizing agents that may be considered as coating substances in the disclosed oral dosage forms are: citric and tartaric acid esters (acetyl-triethyl citrate, acetyl tributyl-, tributyl-, triethyl-citrate); glycerol and glycerol esters (glycerol diacetate, -triacetate, acetylated monoglycerides, castor oil); phthalic acid esters (dibutyl-, diamyl-, diethyl-, dimethyl-, dipropylphthalate), di-(2-methoxy- or 2-ethoxyethyl)-phthalate, ethylphthalyl glycolate, butylphthalylethyl glycolate and butylglycolate; alcohols (propylene glycol, polyethylene glycol of various chain lengths), adipates (diethyladipate, di-(2-methoxy- or 2-ethoxyethyl)-adipate; benzophenone;ATTORNEY DOCKET NO. 320903-2580diethyl- and diburylsebacate, dibutylsuccinate, dibutyltartrate; diethylene glycol dipropionate; ethyleneglycol diacetate, -dibutyrate, -dipropionate; tributyl phosphate, tributyrin; polyethylene glycol sorbitan monooleate (polysorbates such as Polysorbar 50); sorbitan monooleate.

[0151] Moreover, suitable binders, lubricants, disintegrating agents, coloring agents, flavoring agents, flow-inducing agents, and melting agents may be included as carriers. The pharmaceutical carrier employed can be, for example, a solid, liquid, or gas. Examples of solid carriers include, but are not limited to, lactose, terra alba, sucrose, glucose, methylcellulose, dicalcium phosphate, calcium sulfate, mannitol, sorbitol talc, starch, gelatin, agar, pectin, acacia, magnesium stearate, and stearic acid. Examples of liquid carriers are sugar syrup, peanut oil, olive oil, and water. Examples of gaseous carriers include carbon dioxide and nitrogen.

[0152] In various aspects, a binder can include, for example, starch, gelatin, natural sugars such as glucose or beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth, or sodium alginate, carboxymethylcellulose, polyethylene glycol, waxes, and the like. Lubricants used in these dosage forms include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride, and the like. In a further aspect, a disintegrator can include, for example, starch, methyl cellulose, agar, bentonite, xanthan gum, and the like.

[0153] In various aspects, an oral dosage form, such as a solid dosage form, can comprise a disclosed compound that is attached to polymers as targetable drug carriers or as a prodrug. Suitable biodegradable polymers useful in achieving controlled release of a drug include, for example, polylactic acid, polyglycolic acid, copolymers of polylactic and polyglycolic acid, caprolactones, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacylates, and hydrogels, preferably covalently crosslinked hydrogels.

[0154] Tablets may contain the active ingredient in admixture with non-toxic pharmaceutically acceptable excipients which are suitable for the manufacture of tablets. These excipients may be, for example, inert diluents, such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia, and lubricating agents, for example magnesium stearate, stearic acid or talc. The tablets may be uncoated, or they may be coated by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period.

[0155] A tablet containing a disclosed compound can be prepared by compression or molding,ATTORNEY DOCKET NO. 320903-2580optionally with one or more accessory ingredients or adjuvants. Compressed tablets can be prepared by compressing, in a suitable machine, the active ingredient in a free-flowing form such as powder or granules, optionally mixed with a binder, lubricant, inert diluent, surface active or dispersing agent. Molded tablets can be made by molding in a suitable machine, a mixture of the powdered compound moistened with an inert liquid diluent.

[0156] In various aspects, a solid oral dosage form, such as a tablet, can be coated with an enteric coating to prevent ready decomposition in the stomach. In various aspects, enteric coating agents include, but are not limited to, hydroxypropylmethylcellulose phthalate, methacrylic acidmethacrylic acid ester copolymer, polyvinyl acetate-phthalate and cellulose acetate phthalate. Akihiko Hasegawa “Application of solid dispersions of Nifedipine with enteric coating agent to prepare a sustained-release dosage form” Chem. Pharm. Bull. 33:1615-1619 (1985). Various enteric coating materials may be selected on the basis of testing to achieve an enteric coated dosage form designed ab initio to have a preferable combination of dissolution time, coating thicknesses and diametral crushing strength (e.g., see S. C. Porter et al. “The Properties of Enteric Tablet Coatings Made From Polyvinyl Acetate-phthalate and Cellulose acetate Phthalate”, J. Pharm. Pharmacol. 22:42p (1970)). In a further aspect, the enteric coating may comprise hydroxypropyl-methylcellulose phthalate, methacrylic acid-methacrylic acid ester copolymer, polyvinyl acetate-phthalate and cellulose acetate phthalate.

[0157] In various aspects, an oral dosage form can be a solid dispersion with a water soluble or a water insoluble carrier. Examples of water soluble or water insoluble carrier include, but are not limited to, polyethylene glycol, polyvinylpyrrolidone, hydroxypropylmethyl-cellulose, phosphatidylcholine, polyoxyethylene hydrogenated castor oil, hydroxypropylmethylcellulose phthalate, carboxymethylethylcellulose, or hydroxypropylmethylcellulose, ethyl cellulose, or stearic acid.

[0158] In various aspects, an oral dosage form can be in a liquid dosage form, including those that are ingested, or alternatively, administered as a mouth wash or gargle. For example, a liquid dosage form can include aqueous suspensions, which contain the active materials in admixture with excipients suitable for the manufacture of aqueous suspensions. In addition, oily suspensions may be formulated by suspending the active ingredient in a vegetable oil, for example arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. Oily suspensions may also contain various excipients. The pharmaceutical compositions of the present disclosure may also be in the form of oil-in-water emulsions, which may also contain excipients such asATTORNEY DOCKET NO. 320903-2580sweetening and flavoring agents.

[0159] For the preparation of solutions or suspensions it is, for example, possible to use water, particularly sterile water, or physiologically acceptable organic solvents, such as alcohols (ethanol, propanol, isopropanol, 1,2-propylene glycol, polyglycols and their derivatives, fatty alcohols, partial esters of glycerol), oils (for example peanut oil, olive oil, sesame oil, almond oil, sunflower oil, soya bean oil, castor oil, bovine hoof oil), paraffins, dimethyl sulfoxide, triglycerides and the like.

[0160] In the case of a liquid dosage form such as a drinkable solutions, the following substances may be used as stabilizers or solubilizers: lower aliphatic mono- and multivalent alcohols with 2-4 carbon atoms, such as ethanol, n-propanol, glycerol, polyethylene glycols with molecular weights between 200-600 (for example 1 to 40% aqueous solution), diethylene glycol monoethyl ether, 1,2-propylene glycol, organic amides, for example amides of aliphatic C1-C6-carboxylic acids with ammonia or primary, secondary or tertiary C1-C4-amines or C1-C4-hydroxy amines such as urea, urethane, acetamide, N-methyl acetamide, N, N-diethyl acetamide, N, N-dimethyl acetamide, lower aliphatic amines and diamines with 2-6 carbon atoms, such as ethylene diamine, hydroxyethyl theophylline, tromethamine (for example as 0.1 to 20% aqueous solution), aliphatic amino acids.

[0161] In preparing the disclosed liquid dosage form can comprise solubilizers and emulsifiers such as the following non-limiting examples can be used: polyvinyl pyrrolidone, sorbitan fatty acid esters such as sorbitan trioleate, phosphatides such as lecithin, acacia, tragacanth, polyoxyethylated sorbitan monooleate and other ethoxylated fatty acid esters of sorbitan, polyoxyethylated fats, polyoxyethylated oleotriglycerides, linolizated oleotriglycerides, polyethylene oxide condensation products of fatty alcohols, alkylphenols or fatty acids or also 1-methyl-3-(2-hydroxyethyl)imidazolidone-(2). In this context, polyoxyethylated means that the substances in question contain polyoxyethylene chains, the degree of polymerization of which generally lies between 2 and 40 and in particular between 10 and 20. Polyoxyethylated substances of this kind may for example be obtained by reaction of hydroxyl group-containing compounds (for example mono- or diglycerides or unsaturated compounds such as those containing oleic acid radicals) with ethylene oxide (for example 40 Mol ethylene oxide per 1 Mol glyceride). Examples of oleotriglycerides are olive oil, peanut oil, castor oil, sesame oil, cottonseed oil, corn oil. See also Dr. H. P. Fiedler “Lexikon der Hillsstoffe fur Pharmazie, Kostnetik und angrenzende Gebiete” 1971, pages 191-195.ATTORNEY DOCKET NO. 320903-2580

[0162] In various aspects, a liquid dosage form can further comprise preservatives, stabilizers, buffer substances, flavor correcting agents, sweeteners, colorants, antioxidants and complex formers and the like. Complex formers which may be for example be considered are: chelate formers such as ethylene diamine retrascetic acid, nitrilotriacetic acid, diethylene triamine pentacetic acid and their salts.

[0163] It may optionally be necessary to stabilize a liquid dosage form with physiologically acceptable bases or buffers to a pH range of approximately 6 to 9. Preference may be given to as neutral or weakly basic a pH value as possible (up to pH 8).

[0164] In order to enhance the solubility and / or the stability of a disclosed compound in a disclosed liquid dosage form, a parenteral injection form, or an intravenous injectable form, it can be advantageous to employ a-, β- or γ-cyclodextrins or their derivatives, in particular hydroxyalkyl substituted cyclodextrins, e.g. 2-hydroxypropyl-p-cyclodextrin or sulfobutyl-p-cyclodextrin. Also co-solvents such as alcohols may improve the solubility and / or the stability of the compounds according to the present disclosure in pharmaceutical compositions.

[0165] In various aspects, a disclosed liquid dosage form, a parenteral injection form, or an intravenous injectable form can further comprise liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles, and multilamellar vesicles. Liposomes can be formed from a variety of phospholipids, such as cholesterol, stearylamine, or phosphatidylcholines.

[0166] Pharmaceutical compositions of the present disclosure suitable injection, such as parenteral administration, such as intravenous, intramuscular, or subcutaneous administration. Pharmaceutical compositions for injection can be prepared as solutions or suspensions of the active compounds in water. A suitable surfactant can be included such as, for example, hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof in oils. Further, a preservative can be included to prevent the detrimental growth of microorganisms.

[0167] Pharmaceutical compositions of the present disclosure suitable for parenteral administration can include sterile aqueous or oleaginous solutions, suspensions, or dispersions. Furthermore, the compositions can be in the form of sterile powders for the extemporaneous preparation of such sterile injectable solutions or dispersions. In some aspects, the final injectable form is sterile and must be effectively fluid for use in a syringe. The pharmaceutical compositions should be stable under the conditions of manufacture and storage; thus, preferably should beATTORNEY DOCKET NO. 320903-2580preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol and liquid polyethylene glycol), vegetable oils, and suitable mixtures thereof.

[0168] Injectable solutions, for example, can be prepared in which the carrier comprises saline solution, glucose solution or a mixture of saline and glucose solution. Injectable suspensions may also be prepared in which case appropriate liquid carriers, suspending agents and the like may be employed. In some aspects, a disclosed parenteral formulation can comprise about 0.01-0.1 M, e.g. about 0.05 M, phosphate buffer. In a further aspect, a disclosed parenteral formulation can comprise about 0.9% saline.

[0169] In various aspects, a disclosed parenteral pharmaceutical composition can comprise pharmaceutically acceptable carriers such as aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include but not limited to water, alcoholic / aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles can include mannitol, normal serum albumin, sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's and fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Preservatives and other additives may also be present, such as, for example, antimicrobials, antioxidants, collating agents, inert gases and the like. In a further aspect, a disclosed parenteral pharmaceutical composition can comprise may contain minor amounts of additives such as substances that enhance isotonicity and chemical stability, e g., buffers and preservatives. Also contemplated for injectable pharmaceutical compositions are solid form preparations that are intended to be converted, shortly before use, to liquid form preparations. Furthermore, other adjuvants can be included to render the formulation isotonic with the blood of the subject or patient.

[0170] In addition to the pharmaceutical compositions described herein above, the disclosed compounds can also be formulated as a depot preparation. Such long-acting formulations can be administered by implantation (e.g., subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds can be formulated with suitable polymeric or hydrophobic materials (e.g., as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, e.g., as a sparingly soluble salt.ATTORNEY DOCKET NO. 320903-2580

[0171] Pharmaceutical compositions of the present disclosure can be in a form suitable for topical administration. As used herein, the phrase “topical application” means administration onto a biological surface, whereby the biological surface includes, for example, a skin area (e.g., hands, forearms, elbows, legs, face, nails, anus and genital areas) or a mucosal membrane. By selecting the appropriate carrier and optionally other ingredients that can be included in the composition, as is detailed herein below, the compositions of the present invention may be formulated into any form typically employed for topical application. A topical pharmaceutical composition can be in a form of a cream, an ointment, a paste, a gel, a lotion, milk, a suspension, an aerosol, a spray, foam, a dusting powder, a pad, and a patch. Further, the compositions can be in a form suitable for use in transdermal devices. These formulations can be prepared, utilizing a compound of the present disclosure, or pharmaceutically acceptable salts thereof, via conventional processing methods. As an example, a cream or ointment is prepared by mixing hydrophilic material and water, together with about 5 wt% to about 10 wt% of the compound, to produce a cream or ointment having a desired consistency.

[0172] In the compositions suitable for percutaneous administration, the carrier optionally comprises a penetration enhancing agent and / or a suitable wetting agent, optionally combined with suitable additives of any nature in minor proportions, which additives do not introduce a significant deleterious effect on the skin. Said additives may facilitate the administration to the skin and / or may be helpful for preparing the desired compositions. These compositions may be administered in various ways, e.g., as a transdermal patch, as a spot-on, as an ointment.

[0173] Ointments are semisolid preparations, typically based on petrolatum or petroleum derivatives. The specific ointment base to be used is one that provides for optimum delivery for the active agent chosen for a given formulation, and, preferably, provides for other desired characteristics as well (e.g., emollience). As with other carriers or vehicles, an ointment base should be inert, stable, nonirritating and nonsensitizing. As explained in Remington: The Science and Practice of Pharmacy, 19th Ed., Easton, Pa.: Mack Publishing Co. (1995), pp. 1399-1404, ointment bases may be grouped in four classes: oleaginous bases; emulsifiable bases; emulsion bases; and water-soluble bases. Oleaginous ointment bases include, for example, vegetable oils, fats obtained from animals, and semisolid hydrocarbons obtained from petroleum. Emulsifiable ointment bases, also known as absorbent ointment bases, contain little or no water and include, for example, hydroxystearin sulfate, anhydrous lanolin and hydrophilic petrolatum. Emulsion ointment bases are either water-in-oil (W / O) emulsions or oil-in-water (O / W) emulsions, and include, for example, cetyl alcohol, glyceryl monostearate, lanolin and stearic acid. PreferredATTORNEY DOCKET NO. 320903-2580water-soluble ointment bases are prepared from polyethylene glycols of varying molecular weight.

[0174] Lotions are preparations that are to be applied to the skin surface without friction. Lotions are typically liquid or semiliquid preparations in which solid particles, including the active agent, are present in a water or alcohol base. Lotions are typically preferred for treating large body areas, due to the ease of applying a more fluid composition. Lotions are typically suspensions of solids, and oftentimes comprise a liquid oily emulsion of the oil-in-water type. It is generally necessary that the insoluble matter in a lotion be finely divided. Lotions typically contain suspending agents to produce better dispersions as well as compounds useful for localizing and holding the active agent in contact with the skin, such as methylcellulose, sodium carboxymethyl-cellulose, and the like.

[0175] Creams are viscous liquids or semisolid emulsions, either oil-in-water or water-in-oil. Cream bases are typically water-washable, and contain an oil phase, an emulsifier and an aqueous phase. The oil phase, also called the “internal” phase, is generally comprised of petrolatum and / or a fatty alcohol such as cetyl or stearyl alcohol. The aqueous phase typically, although not necessarily, exceeds the oil phase in volume, and generally contains a humectant. The emulsifier in a cream formulation is generally a nonionic, anionic, cationic or amphoteric surfactant. Reference may be made to Remington: The Science and Practice of Pharmacy, supra, for further information.

[0176] Pastes are semisolid dosage forms in which the bioactive agent is suspended in a suitable base. Depending on the nature of the base, pastes are divided between fatty pastes or those made from a single-phase aqueous gel. The base in a fatty paste is generally petrolatum, hydrophilic petrolatum and the like. The pastes made from single-phase aqueous gels generally incorporate carboxymethylcellulose or the like as a base. Additional reference may be made to Remington: The Science and Practice of Pharmacy, for further information.

[0177] Gel formulations are semisolid, suspension-type systems. Single-phase gels contain organic macromolecules distributed substantially uniformly throughout the carrier liquid, which is typically aqueous, but also, preferably, contain an alcohol and, optionally, an oil. Preferred organic macromolecules, i.e., gelling agents, are crosslinked acrylic acid polymers such as the family of carbomer polymers, e.g., carboxypolyalkylenes that may be obtained commercially under the trademark Carbopol™. Other types of preferred polymers in this context are hydrophilic polymers such as polyethylene oxides, polyoxyethylene-polyoxypropylene copolymers and polyvinylalcohol; modified cellulose, such as hydroxypropyl cellulose, hydroxyethyl cellulose,ATTORNEY DOCKET NO. 320903-2580hydroxypropyl methylcellulose, hydroxypropyl methylcellulose phthalate, and methyl cellulose; gums such as tragacanth and xanthan gum; sodium alginate; and gelatin. In order to prepare a uniform gel, dispersing agents such as alcohol or glycerin can be added, or the gelling agent can be dispersed by trituration, mechanical mixing or stirring, or combinations thereof.

[0178] Sprays generally provide the active agent in an aqueous and / or alcoholic solution which can be misted onto the skin for delivery. Such sprays include those formulated to provide for concentration of the active agent solution at the site of administration following delivery, e.g., the spray solution can be primarily composed of alcohol or other like volatile liquid in which the active agent can be dissolved. Upon delivery to the skin, the carrier evaporates, leaving concentrated active agent at the site of administration.

[0179] Foam compositions are typically formulated in a single or multiple phase liquid form and housed in a suitable container, optionally together with a propellant which facilitates the expulsion of the composition from the container, thus transforming it into a foam upon application. Other foam forming techniques include, for example the “Bag-in-a-can” formulation technique. Compositions thus formulated typically contain a low-boiling hydrocarbon, e.g., isopropane. Application and agitation of such a composition at the body temperature cause the isopropane to vaporize and generate the foam, in a manner similar to a pressurized aerosol foaming system. Foams can be water-based or aqueous alkanolic, but are typically formulated with high alcohol content which, upon application to the skin of a user, quickly evaporates, driving the active ingredient through the upper skin layers to the site of treatment.

[0180] Skin patches typically comprise a backing, to which a reservoir containing the active agent is attached. The reservoir can be, for example, a pad in which the active agent or composition is dispersed or soaked, or a liquid reservoir. Patches typically further include a frontal water permeable adhesive, which adheres and secures the device to the treated region. Silicone rubbers with self-adhesiveness can alternatively be used. In both cases, a protective permeable layer can be used to protect the adhesive side of the patch prior to its use. Skin patches may further comprise a removable cover, which serves for protecting it upon storage.

[0181] Examples of patch configuration which can be utilized with the present invention include a single-layer or multi-layer drug-in-adhesive systems which are characterized by the inclusion of the drug directly within the skin-contacting adhesive. In such a transdermal patch design, the adhesive not only serves to affix the patch to the skin, but also serves as the formulation foundation, containing the drug and all the excipients under a single backing film. In the multi-ATTORNEY DOCKET NO. 320903-2580layer drug-in-adhesive patch a membrane is disposed between two distinct drug-in-adhesive layers or multiple drug-in-adhesive layers are incorporated under a single backing film.

[0182] Examples of pharmaceutically acceptable carriers that are suitable for pharmaceutical compositions for topical applications include carrier materials that are well-known for use in the cosmetic and medical arts as bases for e.g., emulsions, creams, aqueous solutions, oils, ointments, pastes, gels, lotions, milks, foams, suspensions, aerosols and the like, depending on the final form of the composition. Representative examples of suitable carriers according to the present invention therefore include, without limitation, water, liquid alcohols, liquid glycols, liquid polyalkylene glycols, liquid esters, liquid amides, liquid protein hydrolysates, liquid alkylated protein hydrolysates, liquid lanolin and lanolin derivatives, and like materials commonly employed in cosmetic and medicinal compositions. Other suitable carriers according to the present invention include, without limitation, alcohols, such as, for example, monohydric and polyhydric alcohols, e.g., ethanol, isopropanol, glycerol, sorbitol, 2-methoxyethanol, diethylene glycol, ethylene glycol, hexyleneglycol, mannitol, and propylene glycol; ethers such as diethyl or dipropyl ether; polyethylene glycols and methoxypolyoxyethylenes (carbowaxes having molecular weight ranging from 200 to 20,000); polyoxyethylene glycerols, polyoxyethylene sorbitols, stearoyl diacetin, and the like.

[0183] Topical compositions of the present disclosure can, if desired, be presented in a pack or dispenser device, such as an FDA-approved kit, which may contain one or more unit dosage forms containing the active ingredient. The dispenser device may, for example, comprise a tube. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser device may also be accompanied by a notice in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions for human or veterinary administration. Such notice, for example, may include labeling approved by the U. S. Food and Drug Administration for prescription drugs or of an approved product insert. Compositions comprising the topical composition of the invention formulated in a pharmaceutically acceptable carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

[0184] Another patch system configuration which can be used by the present invention is a reservoir transdermal system design which is characterized by the inclusion of a liquid compartment containing a drug solution or suspension separated from the release liner by a semi-ATTORNEY DOCKET NO. 320903-2580permeable membrane and adhesive. The adhesive component of this patch system can either be incorporated as a continuous layer between the membrane and the release liner or in a concentric configuration around the membrane. Yet another patch system configuration which can be utilized by the present invention is a matrix system design which is characterized by the inclusion of a semisolid matrix containing a drug solution or suspension which is in direct contact with the release liner. The component responsible for skin adhesion is incorporated in an overlay and forms a concentric configuration around the semisolid matrix.

[0185] Pharmaceutical compositions of the present disclosure can be in a form suitable for rectal administration wherein the carrier is a solid. It is preferable that the mixture forms unit dose suppositories. Suitable carriers include cocoa butter and other materials commonly used in the art. The suppositories can be conveniently formed by first admixing the composition with the softened or melted carrier(s) followed by chilling and shaping in molds.

[0186] Pharmaceutical compositions containing a compound of the present disclosure, and / or pharmaceutically acceptable salts thereof, can also be prepared in powder or liquid concentrate form.

[0187] The pharmaceutical composition (or formulation) may be packaged in a variety of ways. Generally, an article for distribution includes a container that contains the pharmaceutical composition in an appropriate form. Suitable containers are well known to those skilled in the art and include materials such as bottles (plastic and glass), sachets, foil blister packs, and the like. The container may also include a tamper proof assemblage to prevent indiscreet access to the contents of the package. In addition, the container typically has deposited thereon a label that describes the contents of the container and any appropriate warnings or instructions.

[0188] The disclosed pharmaceutical compositions 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. The pack or dispenser may also be accompanied with a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the drug for human or veterinary administration. Such notice, for example, may be the labeling approved by the U. S. Food and Drug Administration for prescription drugs, or the approved product insert. Pharmaceutical compositions comprising a disclosed compound formulated in a compatibleATTORNEY DOCKET NO. 320903-2580pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

[0189] The exact dosage and frequency of administration depends on the particular disclosed compound, a product of a disclosed method of making, a pharmaceutically acceptable salt, solvate, or polymorph thereof, a hydrate thereof, a solvate thereof, a polymorph thereof, or a stereochemically isomeric form thereof; the particular condition being treated and the severity of the condition being treated; various factors specific to the medical history of the subject to whom the dosage is administered such as the age; weight, sex, extent of disorder and general physical condition of the particular subject, as well as other medication the individual may be taking; as is well known to those skilled in the art. Furthermore, it is evident that said effective daily amount may be lowered or increased depending on the response of the treated subject and / or depending on the evaluation of the physician prescribing the compounds of the present disclosure.

[0190] Depending on the mode of administration, the pharmaceutical composition will comprise from 0.05 to 99% by weight, preferably from 0.1 to 70% by weight, more preferably from 0.1 to 50% by weight of the active ingredient, and, from 1 to 99.95% by weight, preferably from 30 to 99.9% by weight, more preferably from 50 to 99.9% by weight of a pharmaceutically acceptable carrier, all percentages being based on the total weight of the composition.

[0191] In one aspect, an appropriate dosage level will generally be about 0.01 to 1000 mg of a compound described herein per kg patient body weight per day and can be administered in single or multiple doses. In various aspects, the dosage level will be about 0.1 to about 500 mg / kg per day, about 0.1 to 250 mg / kg per day, or about 0.5 to 100 mg / kg per day. A suitable dosage level can be about 0.01 to 1000 mg / kg per day, about 0.01 to 500 mg / kg per day, about 0.01 to 250 mg / kg per day, about 0.05 to 100 mg / kg per day, or about 0.1 to 50 mg / kg per day. Within this range the dosage can be 0.05 to 0.5, 0.5 to 5.0 or 5.0 to 50 mg / kg per day. For oral administration, the compositions are preferably provided in the form of tablets containing 1.0 to 1000 mg of the active ingredient, particularly 1.0, 5.0, 10, 15, 20, 25, 50, 75, 100, 150, 200, 250, 300, 400, 500, 600, 750, 800, 900 and 1000 mg of the active ingredient for the symptomatic adjustment of the dosage of the patient to be treated. The compound can be administered on a regimen of 1 to 4 times per day, preferably once or twice per day. This dosing regimen can be adjusted to provide the optimal therapeutic response.

[0192] Such unit doses as described hereinabove and hereinafter can be administered more than once a day, for example, 2, 3, 4, 5 or 6 times a day. In various aspects, such unit doses can beATTORNEY DOCKET NO. 320903-2580administered 1 or 2 times per day, so that the total dosage for a 70 kg adult is in the range of 0.001 to about 15 mg per kg weight of subject per administration. In a further aspect, dosage is 0.01 to about 1.5 mg per kg weight of subject per administration, and such therapy can extend for a number of weeks or months, and in some cases, years. It will be understood, however, that the specific dose level for any particular patient will depend on a variety of factors including the activity of the specific compound employed; the age, body weight, general health, sex and diet of the individual being treated; the time and route of administration; the rate of excretion; other drugs that have previously been administered; and the severity of the particular disease undergoing therapy, as is well understood by those of skill in the area.

[0193] A typical dosage can be one 1 mg to about 100 mg tablet or 1 mg to about 300 mg taken once a day, or multiple times per day, or one time-release capsule or tablet taken once a day and containing a proportionally higher content of active ingredient. The time-release effect can be obtained by capsule materials that dissolve at different pH values, by capsules that release slowly by osmotic pressure, or by any other known means of controlled release.

[0194] It can be necessary to use dosages outside these ranges in some cases as will be apparent to those skilled in the art. Further, it is noted that the clinician or treating physician will know how and when to start, interrupt, adjust, or terminate therapy in conjunction with individual patient response.

[0195] The disclosed pharmaceutical compositions can further comprise other therapeutically active compounds, which are usually applied in the treatment of the above mentioned pathological or clinical conditions.

[0196] It is understood that the disclosed compositions can be prepared from the disclosed compounds. It is also understood that the disclosed compositions can be employed in the disclosed methods of using.

[0197] As already mentioned, the present disclosure relates to a pharmaceutical composition comprising a therapeutically effective amount of a disclosed compound, a product of a disclosed method of making, a pharmaceutically acceptable salt, a hydrate thereof, a solvate thereof, a polymorph thereof, and a pharmaceutically acceptable carrier. Additionally, the present disclosure relates to a process for preparing such a pharmaceutical composition, characterized in that a pharmaceutically acceptable carrier is intimately mixed with a therapeutically effective amount of a compound according to the present disclosure.ATTORNEY DOCKET NO. 320903-2580

[0198] Now having described the aspects of the present disclosure, in general, the following Examples describe some additional aspects of the present disclosure. While aspects of the present disclosure are described in connection with the following examples and the corresponding text and figures, there is no intent to limit aspects of the present disclosure to this description. On the contrary, the intent is to cover all alternatives, modifications, and equivalents included within the spirit and scope of the present disclosure.EXAMPLES

[0199] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices and / or methods claimed herein are made and evaluated and are intended to be purely exemplary of the disclosure and are not intended to limit the scope of what the inventors regard as their disclosure. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in °C or is at ambient temperature, and pressure.

[0200] MATERIALS AND METHODS

[0201] Molecular docking studies: All docking runs for docking DCA on PDK1 and EGFR were performed as flexible docking using MOE (molecular operating environment from the Chemical Computing Group), where side chains were allowed to move freely during the placement of DCA on these proteins. Alpha PMI is the placement method used with default settings (sample per conformation = 10, maximum poses = 250). London dG rescoring was used with Alpha PMI placement. Termination criteria for forcefield refinement were set as gradient = 0.001 and iterations = 500. Protein-protein dockings to create PDK1-EGFR complexes were performed using ClusPro server. Molecular dynamics simulations of PDK1-DCA and EGFR-DCA complexes were done for 40,600 picoseconds using Amber package. The initial 600 picoseconds (ps) of the simulation was for heating and equilibrating the systems, and 40,000 ps was a production run using Isothermal-Isobaric Ensemble at a target temperature of 300 K and pressure of 1 bar using a Langevin thermostat and Berendsen barostat. These simulations were performed using the Velocity-Verlet algorithm (the default algorithm for the Amber MD package). The particle-mesh Ewald (PME) method was used to treat long-range electrostatic interactions using default parameters. To calculate binding energies, MM-GBSA method was used. All water molecules and sodium ions were excluded before MM-GBSA analysis. The values of the dielectric constantATTORNEY DOCKET NO. 320903-2580used for solute and surrounding water were 1 and 80, respectively. MM-GBSA analysis was conducted on 100 snapshots at the interval of 10 ps from the last 1ns of the 40 ns trajectory.

[0202] Compound Synthesis: To a stirred solution of 4,6-di-tert-butyl-2-(hydroxymethyl)-2,3-dihydrobenzofuran-5-ol (0.10 g, 0.36 mmol, 1.00 eq) in DCM (3 ml_) was added Triethylamine (0.10 ml_, 0.72 mmol, 2.00 eq) and Trichloro acetyl chloride (0.045 ml_, 0.40 mmol, 1.10 eq) at 0 °C and continued stirring at 0 °C for 2 h. The reaction was monitored by TLC. After 2 h, the reaction mixture was diluted with DCM (20 mL) washed with water (20 mL), brine solution (20 mL), and dried over anhydrous Na2SO4. Then filtered and the filtrate was concentrated under reduced pressure to give a crude, which was purified by preparative TLC using 10% ethyl acetate in hexane to obtain the final compound (0.01 g, 6.55%) as a cream waxy solid.JVK-26

[0203] Cell culture and reagents: We obtained a U87-MG cell line from the American Type Culture Collection (ATCC, Manassas, VA). These cells were grown in DMEM high glucose media (Hyclone, Logan, UT) supplemented with 10% heat-inactivated FBS (Hyclone), penicillin (100 U / ml), and streptomycin (100 mg / ml) (Life Technologies). Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2. PDK1, EGFR, pEGFR, and GAPDH antibodies were purchased and obtained from Santa Cruz (Santa Cruz, CA) and Novus Biologicals (Centennial, CO). Human astrocytes (#1800) were obtained from the Sciencell laboratories, Carlsbad, CA). PDK inhibitor dichloroacetate (DCA) was from Sigma (St. Louis, MO).

[0204] MTT assay: The proliferation of U87 cells upon JVK-1026 treatment was measured using the 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium-bromide (MTT) (Invitrogen; Carlsbad, CA) assay. We plated around 10,000 cells of U87 and were incubated with vehicle (DMSO), and varying concentrations of JVK-1026 (25nM, 50nM, 100nM, 200nM, 0.5pM, 1pM and 2.5 pM), for 24 h in the 96-well plate. The plate was incubated for 2 h at 37 °C in a CO2 incubator, with 100 pl of MTT reagent to allow the formation of formazan crystals. The medium was replaced with dimethyl sulfoxide (0.1 ml / well), and the 96-well plate was incubated for 30 minutes in a non-CCh incubator. The optical density was read at 550 nm using a Biorad Plate reader.

[0205] Cell Cycle Assay: For cell cycle analysis, we collected both control and JVK-1026 treatedATTORNEY DOCKET NO. 320903-2580U87 cells and were washed with PBS, centrifuged at 1000 rpm for 3 min at room temperature prior to fixation with 70% ethanol and treatment with RNAase (50 pg / mL stock). Cells were subsequently placed in propidium iodide (BioSure, Grass Valley, CA, USA) at 50 pg / mL concentration and incubated for 15 min at 4 °C. The proportion of cells in each phase of the cell cycle was assessed using Cell Quest software (Becton Dickinson Bioscience). To exclude the doublet population, the cells were sequentially gated and then followed up with either an areaheight or an area-width gate using forward scatter.

[0206] Immunoblot analysis: For this analysis, we treated U87 cells with 200nM of JVK-1026 for 48h. The cells were lysed in RIPA lysis buffer supplemented with proteasome and phosphatase inhibitors, and lysates were cleared by centrifugation. Total protein was quantified using the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific, catalog no. 23277). Cell lysates were resolved using SDS-polyacrylamide gel electrophoresis (PAGE). Blots were incubated with respective primary antibodies, followed by incubation with horseradish peroxidase (HRP)-conjugated secondary antibodies. Immuno-reactive bands were visualized using an enhanced chemiluminescent (ECL) reagent. Western blot detection reagents on Hyperfilm MP Autoradiography film (Amersham, Piscataway, NJ). We used PDK1, EGFR, pEGFR and GAPDH at a dilution of 1:1000. GAPDH antibody was used as a loading control.

[0207] RT-PCR analysis: Total RNA was isolated from U87 control and U87-JVK-1206 treated cells after 48h treatment. RT-PCR was conducted using the SYBR green method. The primers used in the study were PDH Forward 5'-TGTTCCTCATCGTACATTCCTCA-3' and Reverse 5'-AGAACTGACATTTTTGCCGTCAA-3'; GAPDH Forward 5’-AATCCCATCACC ATCTTCCA-'3' and Reverse 5'-TGGACTCCACGACGTACTCA-3'3'.

[0208] Metabolic Analysis: To measure Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR), we used the Seahorse XFp Extracellular Flux Analyzer (Seahorse Biosciences, Agilent Technologies). U87 cells were seeded at 40,000 cells per well in XFp 8-well plates with moat chambers. After 24 hours of incubation to allow cell adherence, the cells were treated with 200 nM JVK-1026 or vehicle control. Following a 48-hour treatment period, the culture medium was aspirated, and cells were washed with an assay medium. All reagents and materials for the Seahorse assay were obtained from Seahorse Biosciences (Agilent Technologies). Data analysis was conducted using Wave software (Agilent Technologies), and statistical analysis was performed using GraphPad Prism (10.4).

[0209] Wound Healing and Matriqel Invasion Assays: We performed the wound healing assay toATTORNEY DOCKET NO. 320903-2580study the effect of JVK-1026 on U87 cell motility. For this experiment, around 1 x 106U87 cells were plated on Corning™ BioCoat™ Poly-D-Lysine 6-well plates (cat# 08-774-123) 12 h before the treatment. After 48 h, the monolayers of both cells were scratched using a sterile 200 pl¬ pipette tip with a constant width. Both the control and JVK-1026 cells were photographed at 0 and 12h. The distances were measured using the following formula:Distance migrated = (distance at 0 h - distance at 12 h) / distance at 0 h x 100%.

[0210] Matrigel invasion assay assessed the invasive potential of U87 cells upon JVK-1026 treatment. Both U87 control and JVK-1026 treated cells were seeded at a density of 2 x 105cells per well on the 8 pm pore size upper inserts. DMEM medium with supplements was added to the lower chamber as a chemoattractant. The inserts were then incubated at 37°C. After 24 h, the non invasive cells were removed from the upper surface of the separating membrane by gentle scrubbing with a cotton swab, and the invading cells were fixed in 100% methanol and stained with HEMA-3 stain. The pictograms were captured using an Olympus 1X71 microscope (Center Valley, PA, USA). Both wound healing and matrigel invasion assays were performed in triplicates.

[0211] Detection of Reactive Oxygen Species (ROS): ROS formation was detected using a cell-permeable fluorescent compound, 2', 7'-dichlorofluorescein diacetate (DCFDA). U87 control and JVK-1026 cells were incubated with DCFDA, 20 pM, 100 pl / well) for 30 min at 37°C in the dark. DCFDA, a non-fluorescent compound, can be oxidized by ROS into 2', 7-dichlorofluorescin (DCF), a highly fluorescent compound whose signaling was detected by excitation and emission wavelength at 495 nm and 529 nm, respectively. The experiment was run in triplicate (n=3).

[0212] L- Lactate assay: To measure lactate contents, U87 control and JVK-1026 cells were extracted with cold 80% ethanol (tissue / solvent ratio 1:8) and centrifuged at 10,000 g at 4°C for 30 minutes. The supernatants were collected and diluted with water at different dilutions. The lactate contents were then assayed using the manufacturer’s instructions (Eton Bioscience) using the lactate assay kit.

[0213] Intracranial injections and immunohistochemistry analysis: Around 80,000 U87 cells were injected intracranially on the left side of 5-week-old athymic nude mice (Strain: 002019; Sex: Male; Genotype: Homozygous for Foxn1<nu>); The Jackson Laboratory), under isofluorane anesthesia with the aid of a stereotactic frame. The calvarium of each anesthetized mouse was exposed through a midline incision and a burr hole was drilled 1 mm lateral (left) and 2 mm anterior to the bregma. Two weeks after tumor implantation, the mice were intracranially injected with 1mg of JVK-1026. Following tumor cell injection and treatments, mice were observed daily until theyATTORNEY DOCKET NO. 320903-2580reached a moribund state, at which time they were euthanized and their brains removed and processed for histopathologic analysis. All experiments were approved by the Institutional Animal Care and Use Committee of the University of Illinois College of Medicine Peoria. Next, tumor formation and the phenotype were determined by histologic analysis of hematoxylin and eosin-stained sections. The mouse xenograft tissue (both vehicle-treated and JVK-1026-treated) sections were stained with the PDK1 and pEGFR antibodies as described previously

[0020] , Images were acquired by using an Olympus microscope.

[0214] Statistical Analysis: The results shown are represented as mean ± SD. Graph pad 10.4 was used to perform Student's t-tests and ANOVA to evaluate the differences between the control and treated groups. All p-values were considered statistically significant with a value <0.05.

[0215] RESULTS

[0216] JVK-1026 is a novel and selective inhibitor of PDK1 for targeting GBM cells. Our study aimed to discover new PDK1 inhibitors using an in-silico modeling approach, specifically targeting the critical binding sites of DCA. This effort led to the identification of JVK-1026, a novel and selective PDK1 inhibitor, which exhibited over 100-fold greater potency than DCA, which is currently under clinical evaluation for glioblastoma treatment. We used 10,000 U87 cells treated with JVK-1026 for the initial screening at concentrations of 0.5 mM, 1 mM, and 2.5 mM, respectively (Figure 4A). A dose-dependent decrease in cell viability was observed, with the 0.5 mM concentration achieving a 60% reduction in cell growth. Building on this finding, we conducted a follow-up experiment with 20,000 U87 cells treated with lower concentrations of JVK-1026- 25 pM, 50 pM, 100 pM, and 200 pM (Figure 4B). Remarkably, a 50% reduction in cellular viability was recorded at 100 pM. For comparison, we examined the effects of DCA under similar experimental conditions with concentrations of 25 pM, 50 pM, 100 pM, and 200 pM, noting that despite its historical use at millimolar concentrations, no significant effects on cell viability were observed at these lower doses (Figure 4C). To evaluate the potential neurotoxic effects of JVK-1026, we treated astrocytic cultures with 20,000 cells at concentrations of 100 pM and 200 pM for both JVK-1026 and DCA (Figure 4D &4E). After 48 hours, neither JVK-1026 nor DCA revealed any adverse effects on astrocyte viability. In conclusion, these results suggest that JVK-1026 is a highly effective PDK1 inhibitor capable of targeting glioblastoma cells at substantially lower concentrations than DCA, with no observed neurotoxicity in astrocyte cultures.

[0217] Cell cycle analysis shows selective G2 / M arrest in U87 cells. Cell cycle analysis is a crucial method for studying the efficacy and mechanism of action of novel inhibitors, specificallyATTORNEY DOCKET NO. 320903-2580regarding how JVK-1026 influences GBM cell proliferation, division, and death. In our experiment, U87 cells were treated with 100 pM JVK-1026 or 100 M DCA for 48 hours, revealing that JVK-1026 decreased the percentage of cells in the G1 phase from 73.39% to 58.05% (a 17.28% reduction), increased the S phase from 5.5% to 7.2% (a 29.49% increase), and raised the G2 / M phase from 14.86% to 22.43% (a 50.94% increase) (Figure 5A). These results align with previous studies indicating cell cycle arrest in the G2 / M phase following treatment with metabolic inhibitors and temozolomide. Conversely, DCA treatment at 100 pM displayed no noticeable effect on the cell cycle distribution (Figure 5B). To assess the potential toxicity of JVK-1026 at the cell cycle level, we performed a parallel experiment on astrocytic cultures using the same concentration, where JVK-1026 did not alter the cell cycle profile or distribution, suggesting a selective effect on glioblastoma cells (Figure 5C).

[0218] JVK-1026 decreases PDK1 expression and promotes a shift toward oxidative phosphorylation. To investigate the impact of JVK-1026 on PDK1 and its downstream signaling in U87 cells, we performed western blotting and metabolic assays. U87 cells were treated with JVK-1026, and the expression of PDK1, EGFR, and phosphorylated EGFR (pEGFR) was analyzed. Western blot analysis revealed a significant reduction in PDK1 protein levels following JVK-1026 treatment compared to control cells (Figure 6A). Quantification of band intensities confirmed that JVK-1026 decreased PDK1 expression by approximately 80% (p < 0.0001). Interestingly, while total EGFR levels remained unchanged, phosphorylated EGFR (pEGFR) was markedly reduced by over 90% upon JVK-1026 treatment (p < 0.001). Next, to assess the effect of PDK1 inhibition on cellular metabolism, we measured the activity of pyruvate dehydrogenase (PDH), a key enzyme regulated by PDK1, as well as the levels of tricarboxylic acid (TCA) cycle intermediates. As shown in Figure 6B, JVK-1026 treatment significantly increased PDH activity by approximately 5-fold compared to control cells (p = 0.001), indicating enhanced conversion of pyruvate to acetyl-CoA. Additionally, the levels of o-ketoglutarate (a-KG) and citrate synthase (CS) activity were also elevated by approximately 2-fold and 1.5-fold, respectively, in response to JVK-1026 (p = 0.02 for both), suggesting an upregulation of TCA cycle flux.

[0219] JVK-1026 reduces glycolytic activity in U87 Cells. To investigate the effects of JVK-1026 on metabolic reprogramming and signaling pathways in GBM, we performed a Seahorse XFp analysis to assess extracellular acidification rate (ECAR) and oxygen consumption rate (OCR). In this study, the U87 cells were treated with 100 pM JVK-1026, and the impact on glycolysis and oxidative phosphorylation was analyzed. As shown in Figure 7A, JVK-1026-treated cells displayed a marked decrease in ECAR compared to control cells over time, which implies that theATTORNEY DOCKET NO. 320903-2580treatment significantly reduced the glycolytic capacity of U87. Further quantification of glycolytic parameters demonstrated a reduction in both glycolysis and glycolytic capacity, with no significant change observed in glycolytic reserve (Figure 7B). Specifically, glycolysis decreased from 150 mpH / min in control cells to approximately 120 mpH / min in JVK-1026-treated cells, while glycolytic capacity dropped from 180 mpH / min to around 140 mpH / min. Next, we assessed the reactive oxygen species (ROS) Production in U87 Cells after treatment with 100 pM JVK-1026. As shown in Figure 7C, JVK-1026 significantly increased ROS levels in U87 cells by approximately 2.3-fold compared to control cells (p = 0.00007). This elevation in ROS suggests that JVK-1026 induces oxidative stress, potentially contributing to its anti-tumor effects. To measure the impact of JVK-1026 on glycolysis, we measured lactate release from U87 cells. We showed that treatment with 100 pM JVK-1026 significantly decreased lactate production by approximately 40% compared to control cells (p = 0.001). This reduction in lactate release indicates that JVK-1026 inhibits glycolytic activity in U87 cells (Figure 7D).

[0220] JVK-1026 inhibits U87 cell migration more effectively than DCA. T o assess the effects of JVK-1026 on U87 glioblastoma cell migration, we performed a wound healing assay. U87 cells were treated with 100 pM JVK-1026 or 100 pM dichloroacetate (DCA) for 12 hours, and the rate of wound closure was measured using Olympus Microscopy. The control cells exhibited substantial migration, with the wound width decreasing from 735.30 pM at 0 hours to 122.77 pM after 12 hours. In contrast, JVK-1026 treatment significantly inhibited cell migration, as the wound width only decreased from 733.69 pM to 390.22 pM over the same period. DCA treatment resulted in a moderate reduction in wound width (from 733.69 pM to 198.34 pM), but this effect was less pronounced compared to JVK-1026. Quantification of the wound closure confirmed that JVK-1026 was more effective at inhibiting U87 cell migration than DCA, suggesting that JVK-1026 may have stronger anti-migratory properties in GBM cells (Figure 8).

[0221] JVK-1026 inhibits U87 cell invasion more compared to DCA. Next, we evaluated the effect of JVK-1026 on U87 cell invasion using a matrigel-plug transwell invasion assay. The control cells exhibited a high invasive capacity. Treatment with 100 pM JVK-1026 significantly reduced the number of invading cells, representing an 83% reduction in invasion. In comparison, DCA treatment at the same concentration reduced invasion but was less effective than JVK-1026 (Figure 9). These results demonstrate that JVK-1026 is more potent in inhibiting U87 cell invasion than DCA, highlighting its potential as a stronger therapeutic agent for limiting GBM cell invasiveness.ATTORNEY DOCKET NO. 320903-2580

[0222] JVK-1026 prolongs survival in U87 GBM mouse model: To evaluate the efficacy of JVK-1026 in prolonging survival and reducing tumor burden in glioblastoma, we implanted 80,000 U87 glioblastoma cells intracranially into 14 mice. On day 13, the mice were randomized based on their weights into two groups: one receiving vehicle control (DMSO) and the other receiving 1 mg of JVK-1026. The survival rates were assessed by plotting Kaplan-Meier survival analysis (Figure 10A). We observed that JVK-1026 treatment significantly extended the survival of mice compared to the vehicle control group. All control mice succumbed to tumor burden by day 17, while JVK-1026-treated mice exhibited prolonged survival, with some surviving up to 24 days postimplantation. These results indicate that JVK-1026 effectively improves longevity in this glioblastoma model. We monitored mouse body weights throughout the study to indicate general health (Figure 10B). Control mice experienced a rapid decline in weight starting around day 15, correlating with tumor progression. In contrast, JVK-1026-treated mice maintained stable weights until day 20, after which a gradual decline was observed. This suggests that JVK-1026 delays tumor-associated weight loss and maintains overall health longer than vehicle-treated controls. Upon induction of animal endpoints, the mouse was euthanized, and the brains were collected for further examination. Hematoxylin and eosin (H& E) staining of brain sections from both groups revealed a marked reduction in tumor size in the JVK-1026-treated group compared to controls. Vehicle-treated mice displayed large, invasive tumors occupying significant regions, while JVK-1026-treated mice exhibited smaller and less invasive tumors. This reduction in tumor size further supports the therapeutic potential of JVK-1026. We then checked if JVK-1026 reduces PDK1 and pEGFR expression, and we performed an immunohistochemistry (IHC) assay. In vehicle-treated tumors, we recorded strong positive staining for PDK1 and pEGFR was observed, indicating active signaling pathways driving tumor progression. In contrast, tumors from J VK-1026-treated mice showed markedly reduced staining for both PDK1 and pEGFR, suggesting that JVK-1026 effectively inhibits these pathways in vivo. In summary, these results demonstrate that treatment with JVK-1026 significantly prolongs survival, maintains body weight, reduces tumor burden, and downregulates key oncogenic markers such as PDK1 and pEGFR in a U87 glioblastoma mouse model. These findings highlight the potential of JVK-1026 as a promising therapeutic agent for glioblastoma treatment.

[0223] In vitro efficacy of JVK 1009 targeting PDK1 in Medulloblastoma: Figures 12A-12C show the in vitro testing of JVK 1009 targeting PDK1 in MB cell lines. (A, B & C) MTT assay showing the effects of PDK1 inhibitors (0.01-1 pM) on MB (p=0.0001) and astrocyte cell viability (n.s). The data are presented as mean values, with error bars representing standard deviation (n=5). FigureATTORNEY DOCKET NO. 320903-258012D shows the ECAR analysis using JVK 1009, which assesses shifts in glycolysis and mitochondrial respiration. Data are presented as mean values, with error bars as standard deviation showing changes in cellular metabolic behavior after MB cell treatment (n=3). The results show that JVK 1009 is more effective in the inhibition of PDK1 compared to DCA.

[0224] DISCUSSION

[0225] The results of this study establish JVK-1026 as a potent and selective inhibitor of PDK1, with significant therapeutic potential for treating glioblastoma (GBM). Our research highlights the efficacy of JVK-1026 in reducing cell viability, inducing cell cycle arrest, reprogramming metabolic pathways, inhibiting migration and invasion, and prolonging survival in preclinical models of GBM, particularly U87 cells.

[0226] One of the significant findings was the marked reduction in cell viability observed upon treatment with JVK-1026 at lower concentrations compared to dichloroacetate (DCA) at historically higher concentrations. In our initial screening, JVK-1026 demonstrated dosedependent anti-proliferative effects, with a substantial reduction in viability at concentrations as low as 0.5 mM, achieving about a 60% decrease in growth. This decrease was even more pronounced at 100 pM, where a 50% reduction in cell viability was observed. In stark contrast, DCA, which has been extensively studied and utilized in high millimolar concentrations due to its role as a metabolic inhibitor, did not exhibit significant effects at lower concentrations (25 pM to 200 pM). This situation underscores that JVK-1026 not only possesses enhanced potency but also achieves effective results at concentrations that may minimize potential toxicity, making it a promising candidate for therapeutic application.

[0227] Our cell cycle analysis revealed that JVK-1026 treatment led to a selective G2 / M arrest in U87 cells, correlating with previous findings that metabolic inhibitors can disrupt normal cell cycle progression. The significant shift in cell distribution — from a decrease in the G1 phase and an increase in both the S and G2 / M phases — indicates that JVK-1026 may interfere with cell cycle checkpoints, ultimately promoting cell death. In contrast, DCA did not show a noticeable effect on cell cycle distribution, suggesting that its impact may be context-dependent and limited in efficacy when not utilized at high concentrations.

[0228] Further investigations into the mechanism of action of JVK-1026 showed its ability to significantly downregulate PDK1 expression and modulate associated pathways. Treatment with JVK-1026 achieved an approximately 80% decrease in PDK1 expression, as well as a notable reduction in phosphorylated EGFR (pEGFR) levels. This reduction is particularly noteworthyATTORNEY DOCKET NO. 320903-2580because pEGFR is known to activate downstream survival signaling pathways, thus promoting tumor progression. The enhanced activity of pyruvate dehydrogenase (PDH) and upregulated tricarboxylic acid (TCA) cycle intermediates further suggest that JVK-1026 not only curtails glycolytic metabolism but actively promotes oxidative phosphorylation. This shift in metabolic state towards more efficient energy production could contribute to the therapeutic effects observed in GBM models.

[0229] The Seahorse XFp analysis confirmed these metabolic changes, where JVK-1026 treatment led to decreased extracellular acidification rates (ECAR) and reduced lactate release, corroborating its role in inhibiting glycolytic activity. The increase in reactive oxygen species (ROS) levels induced by JVK-1026 signifies the potential of inducing oxidative stress in tumor cells, a mechanism that can be exploited to enhance the anti-tumor effects. This oxidative stress could be a double-edged sword; while it can lead to increased apoptosis in cancer cells, careful consideration must be given to the potential impact on surrounding normal tissues.

[0230] Moreover, the effects of JVK-1026 on cell migration and invasion highlight its role as a strong anti-metastatic agent. The wound healing assay and transwell invasion assays demonstrated that JVK-1026 significantly inhibited U87 cell migration and invasion, outperforming DCA. The pronounced invasion reduction further establishes JVK-1026 as not only a growth inhibitor but also a powerful agent against the invasive nature of glioblastoma.

[0231] In vivo experiments further reinforced the promising therapeutic potential of JVK-1026, showing that it significantly prolonged survival in U87 GBM-bearing mice while maintaining body weight and reducing tumor burden. The reduction in tumor size and diminished expression of oncogenic markers such as PDK1 and pEGFR in JVK-1026-treated mice reiterates its efficacy in modulating critical pathways involved in GBM progression.

[0232] In summary, our findings indicate that JVK-1026 is a highly effective and selective PDK1 inhibitor that significantly impacts GBM cell viability, metabolic programming, cell cycle dynamics, and invasive properties, demonstrating superior effects compared to DCA at lower concentrations. The favorable safety profile and potent anti-tumor effectiveness advocate for further development and clinical evaluation of JVK-1026 as a novel therapeutic strategy for glioblastoma, potentially overcoming limitations associated with existing treatment modalities, including those linked to DCA's higher concentration application and resultant side effects.

[0233] It should be emphasized that the above-described embodiments of the present disclosure are merely possible examples of implementations set forth for a clear understanding of theATTORNEY DOCKET NO. 320903-2580principles of the disclosure. Many variations and modifications may be made to the abovedescribed embodiment(s) without departing substantially from the spirit and principles of the disclosure. All such modifications and variations are intended to be included herein within the scope of this disclosure and protected by the following claims.ATTORNEY DOCKET NO. 320903-2580REFERENCES1. Davis ME: Glioblastoma: Overview of Disease and Treatment Clin J Oncol Nurs 2016, 20(5 Suppl):2.2. 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Ohgaki H, Dessen P, Jourde B, Horstmann S, Nishikawa T, Di Patre P, Burkhard C, Schuler D, Probst-Hensch NM, Maiorka PC, Baeza N, Pisani P, Yonekawa Y, Yasargil MG, Lutolf UM, Kleihues P: Genetic pathways to glioblastoma: a population-based study. Cancer Res 2004, 64(19):6892-6899.9. Rabah N, Ait Mohand F, Kravchenko- Balasha N: Understanding Glioblastoma Signaling, Heterogeneity, Invasiveness, and Drug Delivery Barriers. Int J Mol Sci 2023, 24(18):14256. doi: 10.3390 / ijms241814256.10. Garcia-Montano LA, Licon-Munoz Y, Martinez FJ, Keddari YR, Ziemke MK, Chohan MO, Piccirillo SGM: Dissecting Intra-tumor Heterogeneity in the Glioblastoma Microenvironment Using Fluorescence-Guided Multiple Sampling. Mol Cancer Res 2023, 21(8):755-767.ATTORNEY DOCKET NO. 320903-258011. 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Int J Mol Sci 2021, 22(14):7265. doi: 10.3390 / ijms22147265.20. Velpula KK, Guda MR, Sahu K, Tuszynski J, Asuthkar S, Bach SE, Lathia JD, Tsung AJ: Metabolic targeting of EGFRvIII / PDK1 axis in temozolomide resistant glioblastoma. Oncotarget 2017, 8(22): 35639-35655.21. El Khayari A, Bouchmaa N, Taib B, Wei Z, Zeng A, El Fatimy R: Metabolic Rewiring in Glioblastoma Cancer: EGFR, IDH and Beyond. Front Oncol 2022, 12:901951.22. Tataranni T, Piccoli C: Dichloroacetate (DCA) and Cancer: An Overview towards Clinical Applications. Oxid Med Cell Longev 2019, 2019:8201079.23. Faubert B, Solmonson A, DeBerardinis RJ: Metabolic reprogramming and cancer progression. Science 2020, 368(6487): 10.1126 / science.aaw5473.ATTORNEY DOCKET NO. 320903-258024. de Mey S, Dufait I, Jiang H, Corbet C, Wang H, Van De Gucht M, Kerkhove L, Law KL, Vandenplas H, Gevaert T, Feron O, De Ridder M: Dichloroacetate Radiosensitizes Hypoxic Breast Cancer Cells. 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Claims

1. ATTORNEY DOCKET NO. 320903-2580CLAIMS1. A compound of formula I or a pharmaceutically acceptable salt thereofWherein- represents a single or double bond;Y is C or NR3, wherein R3is absent, hydrogen, or an alkyl group;Z is C or N;R1and R2together with the atoms to which they are attached form an aryl ring, a heteroaryl ring, a cycloalkyl ring, or heterocycloalkyl ring, orR1and R2are independently (i) a substituted alkyl group or an unsubstituted alkyl group; (ii) a substituted alkenyl group or an unsubstituted alkenyl group; (iii) a thioalkyl group; (iv) an aminoalkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted heteroaryl group or an unsubstituted heteroaryl group; (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group, provided that R1and R2are not both H; andwhereinATTORNEY DOCKET NO.320903-2580R4and R5are, independently, (i) a haloalkyl group (ii) hydrogen, (iii) a substituted heteroaryl group or an unsubstituted heteroaryl group; (iv) a substituted alkyl group or an unsubstituted alkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted alkenyl group or an unsubstituted alkenyl group; (vii) a substituted cycloalkyl group or an unsubstituted cycloalkyl group; or (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group; the stereochemistry at a is racemic, substantially R, or substantially S; the stereochemistry at b is racemic, substantially R, or substantially S; and the stereochemistry at c is racemic, substantially R, or substantially S.

2. The compound of claim 1, wherein Z is C.

3. The compound of claim 1 or 2, wherein Y is C.

4. The compound of any one of claims 1-3, wherein - represents a single bond.

5. The compound of any one of claims 1 -4, wherein R1and R2together with the atoms to which they are attached form a heterocycloalkyl ring, wherein the heterocycloalkyl ring is optionally fused with a (i) a substituted heteroaryl group or an unsubstituted heteroaryl group or (ii) a substituted aryl group or an unsubstituted aryl group.

6. The compound of any one of claims 1-5, wherein X is -CH2OH orOwherein R4is haloalkyl.

7. The compound of claim 1, wherein the compound is one of the following structureswhereinn is an integer from 1 to 4; andeach R6is independently selected from hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group,ATTORNEY DOCKET NO.320903-2580a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orIIIwherein R7 and R9 are C1-C6 alkyl, R8 is hydroxy or alkoxy, and R4is haloalkyl; orWhereinn is an integer from 1 to 4; andR4and each R10is independently selected from hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orVwhereinR10 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andATTORNEY DOCKET NO.320903-2580R4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orVIwhereinR11 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orWhereinR11 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted alkenylATTORNEY DOCKET NO.320903-2580group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; orwhereinR11 is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group; andR4is hydrogen, alkyl, alkenyl, hydroxy, alkoxy, aryl, aryloxy, a substituted or unsubstituted heteroaryl group, an amino group, a substituted amino group, a substituted or unsubstituted cycloalkyl group, a substituted or unsubstituted alkenyl group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted heterocycloalkyl group.

8. The compound of claim 7, wherein when the compound has the formula II, each of R6is hydrogen.

9. The compound of claim 8, wherein n is 3, wherein a first Reis hydroxy and a second and third R6is a C1-C6 alkyl group.

10. The compound of claim 7 or 8, wherein X is -CH2OH orR.wherein R4is haloalkyl.

11. The compound of claim 10, wherein R4is a C1 to C5 perhalogenated alkyl group.

12. The compound of claim 10, wherein R4is CF3 or CCI3.

13. The compound of claim 7, wherein when the compound has the formula III, R? and R9 are each tert-butyl and R8is hydroxy.

14. The compound of claim 13, wherein R4is CCI3.

15. The compound of claim 13 or 14, wherein the stereochemistry at carbon b is substantially R or S.ATTORNEY DOCKET NO.320903-258016. The compound of claim 7, wherein when the compound has the formula VI, VII, or VIII, R4is a substituted or unsubstituted aryl group or a substituted or unsubstituted heteroaryl group and Rn is hydrogen or a substituted or unsubstituted aryl group or a substituted or unsubstituted heteroaryl group.

17. The compound of claim 1, wherein the compound has one of the following structureswhereinR2is (i) a substituted alkyl group or an unsubstituted alkyl group; (ii) a substituted alkenyl group or an unsubstituted alkenyl group; (iii) a thioalkyl group; (iv) an aminoalkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted heteroaryl group or an unsubstituted heteroaryl group; or (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group;the stereochemistry at a is racemic, substantially R, or substantially S; the stereochemistry at b is racemic, substantially R, or substantially S; and R4is haloalkyl; orR4XwhereinR1and R2together with the atoms to which they are attached form an aryl ring, a heteroaryl ring, a cycloalkyl ring, or heterocycloalkyl ring;the stereochemistry at b is racemic, substantially R, or substantially S; and R4is haloalkyl; orATTORNEY DOCKET NO.320903-2580whereinZ is CH, N, or NH+;Ri is (i) a substituted alkyl group or an unsubstituted alkyl group; (ii) a substituted alkenyl group or an unsubstituted alkenyl group; (iii) a thioalkyl group; (iv) an aminoalkyl group; (v) a substituted aryl group or an unsubstituted aryl group; (vi) a substituted heteroaryl group or an unsubstituted heteroaryl group; (vii) a substituted heterocycloalkyl group or an unsubstituted heterocycloalkyl group;R is haloalkyl;the stereochemistry at b is racemic, substantially R, or substantially S; and the stereochemistry at c is racemic, substantially R, or substantially S.

18. The compound of claim 1, wherein the compound isATTORNEY DOCKET NO.320903-2580ATTORNEY DOCKET NO.320903-2580ATTORNEY DOCKET NO.320903-2580ATTORNEY DOCKET NO.320903-2580ATTORNEY DOCKET NO.320903-2580OCF3ATTORNEY DOCKET NO.320903-258019. The compound of claim 1, wherein the compound isATTORNEY DOCKET NO.320903-2580ATTORNEY DOCKET NO.320903-2580ATTORNEY DOCKET NO.320903-2580or / 20. A pharmaceutical composition comprising a pharmaceutically acceptable carrier and a compound of any one of claims 1-19.

21. A method of treating cancer in a subject, the method comprising administering to the subject an effective amount of the compound of any one of claims 1-19.

22. The method of claim 21, wherein the cancer is associated with an elevated level of pyruvate dehydrogenase kinase 1 (PDK1) in the subject.

23. The method of claim 21, wherein the cancer comprises glioblastoma, medulloblastoma, or breast cancer.

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