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AU2013230881A1 - Selective histone deactylase 6 inhibitors - Google Patents

Selective histone deactylase 6 inhibitors Download PDF

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AU2013230881A1
AU2013230881A1 AU2013230881A AU2013230881A AU2013230881A1 AU 2013230881 A1 AU2013230881 A1 AU 2013230881A1 AU 2013230881 A AU2013230881 A AU 2013230881A AU 2013230881 A AU2013230881 A AU 2013230881A AU 2013230881 A1 AU2013230881 A1 AU 2013230881A1
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compound
aryl
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heteroaryl
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AU2013230881A
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Joel Bergman
Alan Kozikowski
Eduardo M. Sotomayor
Alejandro V. VILLAGRA
Karrune Veeraprasert WOAN
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H Lee Moffitt Cancer Center and Research Institute Inc
University of Illinois at Urbana Champaign
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H Lee Moffitt Cancer Center and Research Institute Inc
University of Illinois at Urbana Champaign
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Abstract

Disclosed are selective histone deactylase inhibitors (HDACi) that having Formula (I). Methods of making and using these inhibitors for the treatment of cancer, in particular melanoma are also disclosed.

Description

WO 2013/134467 PCT/US2013/029521 SELECTIVE HISTONE DEACTYLASE 6 INHIBITORS ACKNOWLEDGEMENT OF GOVERNMENT SUPPORT This invention was made with government support from the National Institutes of Health 5 under Grant number CA134807. The government has certain rights in this invention. CROSS REFERENCE TO REALTED APPLICATIONS This application claims the benefit of priority to U.S. Provisional Application No. 61/607,083 filed March 7, 2012; U.S. Provisional Application No. 61/618,150, filed March 30, 2012; U.S. Provisional Application No. 61/648,946, filed May 18, 2012; U.S. Provisional 10 Application No. 61/651,595, filed May 25, 2012; U.S. Provisional Application No. 61/651,896, filed May 25, 2012; U.S. Provisional Application No. 61/674,942, filed July 24, 2012; and U.S. Provisional Application No. 61/715,379, filed October 18, 2012, all of which are incorporated by reference herein in their entirities. BACKGROUND 15 Epigenetic regulation and subsequent gene expression or silencing represents a tightly orchestrated interplay among enzymes responsible for modifying the tails of histones, around which nuclear DNA is wrapped. Among the various modifiers of the histones, the cell is capable of balancing the activity of both histone acetyltransferases (HAT) and histone deacetylases (HDAC) to attach or remove the acetyl group, respectively, from the lysine tails of these histone 20 barrels. This particular epigenetic marker masks the positive lysine residues from interacting closely with the DNA phosphate-backbone, resulting in a more "open" chromatin state, whereas the deacetylases remove these acetyl groups, resulting in a more "closed" or compacted DNA histone state. There are currently no selective HDAC6 inhibitors (HDAC6i) approved for oncology 25 purposes. Such molecules would be advantageous as a therapeutic approach for they can result in reduced side effects, which is an apparent problem associated with less selective HDACIs (Zhang et al., "Mice lacking histone deacetylase 6 have hyperacetylated tubulin but are viable and develop normally," Mol Cell Biol 2008, 28(5):1688-1701). Recent pre-clinical efforts are being directed toward the use of HDAC6i for certain cancers, specifically in combination with 30 known drugs (Santo et al., "Preclinical activity, pharmacodynamic, and pharmacokinetic properties of a selective HDAC6i, ACY-1215, in combination with bortezomib in multiple myeloma," Blood 2012, 119(11):2579-2589). HDACIs can be useful as possible therapeutics for melanoma; however, studies to date have focused on using pan-HDACIs, such as suberoylanilide hydroxamic acid (SAHA) (Peltonen et al., "Melanoma cell lines are susceptible 35 to histone deacetylase inhibitor TSA provoked cell cycle arrest and apoptosis," Pigment Cell Res 1 WO 2013/134467 PCT/US2013/029521 2005, 18(3):196-202; Facchetti et al., "Modulation of pro- and anti-apoptotic factors in human melanoma cells exposed to histone deacetylase inhibitors," Apoptosis 2004, 9(5):573-582). While SAHA exhibits activity against all Zn-dependant HDAC isozymes, it has been approved solely for the treatment of cutaneous T cell lymphoma (Wagner et al., "Histone deacetylase 5 (HDAC) inhibitors in recent clinical trials for cancer therapy," Clinical Epigenetics 2010, 1(3 4):117-136). It has previously been reported that HDAC6 forms an association with HDAC1 1 (Gao et al., "Cloning and functional characterization of HDAC 11, a novel member of the human histone deacetylase family," JBiol Chem 2002, 277(28):25748-25755). Recent efforts have begun to uncover the biological significance of HDAC 11 as a participant in activating the 10 immune response and targeting one or both of these enzymes is of therapeutic value (Villagra et al., "The histone deacetylase HDAC 11 regulates the expression of interleukin 10 and immune tolerance," Nat Immunol 2009, 10(1):92-100; Wang et al., "Histone Deacetylase Inhibitor LAQ824 Augments Inflammatory Responses in Macrophages through Transcriptional Regulation of IL-10," Jmmunol 2011, 186(7):3986-3996). Thus, HDAC6 has emerged as a 15 target in the treatment of melanoma and other cancers. Such an approach can be devoid of the cytotoxic properties of the pan-HDACi's and thus of value in the context of safer cancer therapeutics (Parmigiani et al., "HDAC6 is a specific deacetylase of peroxiredoxins and is involved in redox regulation," Proc Nat A cad Sci USA 2008, 105(28):9633-9638). What are needed then are new and selective HDAC6 inhibitors and methods of making and using them to 20 treat various cancers as well as to augment various tumor immune responses. The compositions and methods disclosed herein address these and other needs. BRIEF DESCRIPTION OF FIGURES The accompanying figures, which are incorporated in and constitute a part of this specification, illustrate several aspects described below. 25 Figure 1 is an image depicting the grouping oflIDACs. Figure 2 is an image depicting HDACs are targets for histone deacetylase inhibitors (HDACi). Figure 3 is an image depicting HDAC6 was found to influence the IL-10 gene expression in APCs. 30 Figure 4 is an image depicting the genetic or pharmacologic disruption of HDAC6 inhibits IL-IO. Figure 5 is an image depicting the genetic disruption of HDAC6 enhances APC function. Figure 6 is an image depicting mechanisms as shown by CHIP analysis oflL-lO gene promotor in macrophages include H3 and H4 acetylation; HDAC6 recruitment; and binding of 35 STAT3 and other transcription factors at several timepoints after LPS stimulation. 2 WO 2013/134467 PCT/US2013/029521 Figure 7 is an image depicting that knocking down HDAC6 results in a decreased recruitment of the transcriptional activator STAT3 to the IL-10 gene promotor. Figure 8 is an image depicting disruption of STAT3 binding to the gene promoter resulted in decreased recruitment of HDAC6 and diminished IL-10 production. 5 Figure 9 is an image depicting disruption of HDAC6 inhibits STAT3 phosphorylation. Figure 10 is a series of images depicting that increased expression of HDAC6 and IL 1 OmRNA in human melanoma. Figure 11 is a series of images that illustrate HDAC6 expression in murine and human melanoma cell lines. 10 Figure 12 is a series of images depicting HDAC protein expression in melanoma. Figure 13 is a series of images depicting decreased proliferation and cell cycle arrest in melanoma cells lacking HDAC6. Figure 14 is a series of images depicting melanoma cells lacking in HDAC6 are more Immunogemc. 15 Figure 15 is a series of images depicting the pharmacologic inhibition of HDAC6 in melanoma cells resulted in cell cycle arrest and increased expression of MHC molecules. Figure 16 is an image depicting tubastatin-A inhibits JAK2/STA T3 phosphorylation in B16 murine melanoma cells in vivo. Figure 17 is a series of images depicting tubastatin A augments antigen-specific CD4+T 20 -cell responses to vaccination in melanoma bearing mice. Figure 18 is an image depicting tubastatin A, a selective HDAC6 inhibitor decreased STAT3 phosphorylation and recruitment to the IL-10 gene promotor in APCs. Figure 19 is an image depicting the phenotypic and functional changes in APCs treated with Tubastatin A. 25 Figure 20 is an image depicting tubastatin A-treated APCs are better activators of naIve T -cells and restore the responsiveness of anergic T cells. Figure 21 is a graph depicting the antitumor effect of tubastatin A in vivo. Figure 22 is a series of images depicting that tubastatin A does not affect PEM. Figure 23 is a series of images depicting the immunological effects of Tubastatin A upon 30 macrophages. Figure 24 is a series of images depicting Tubastatin A inhibits IL-I0 transcription by disrupting the JAKISTAT3 pathway in macrophages. Figure 25 is a graph depicting the inhibitory effect of tubastatin A upon IL-I0 production is lost in the absence ofHDAC6. 3 WO 2013/134467 PCT/US2013/029521 Figure 26 is a flow chart depicting the experimental design of the in vitro antigenpresenting studies. Figure 27 is a series of images depicting that tubastatin A treated macrophages are better activators of naIve T -cells and restore function of anergic T -cells. 5 Figure 28 is a series of images depicting in vivo treatment with tubastatin A augment the response of antigen-specific T-cell to vaccination. Figure 29 is an image depicting HDAC6 expression in human MCL. Figure 30 is a series of images depicting the disruption ofHDAC6 in human MCL cell lines. 10 Figure 31 is an image depicting the disruption of HDAC6 in murine FC-muMCLI cells. Figure 32 is an image depicting the immunological effects of HDAC6 inhibition in MCL. Changes in MHC, co-stimulatory molecules and/or cytokine production in response to LPS or CpG +/- ST-3-06 or Tubastatin A are show. Figure 33 is a series of images depicting the antigen-presenting function of FCmuMCLI 15 cells treated with ST-3-06. Figure 34 is a senes of images depicting the antigen-presenting function of FCmuMCLl cells treated with tubastatin A. Figure 35 is an image depicting the antitumor effect of tubas tat in A in vivo. Figure 36 is a series of images depicting the disruption of HDAC6 inhibits STAT3 20 phosphorylation in APCs. Figure 37 is a series of images depicting ST -3-06 decreased STAT3 phosphorylation and recruitment to the IL-10 gene promotor in APCs. Figure 38 is a Western blot showcasing substrate specificity of 5g. SUMMARY 25 In accordance with the purposes of the disclosed materials, compounds, compositions, articles, devices, and methods, as embodied and broadly described herein, the disclosed subject matter relates to compositions and methods of making and using the compositions. In other aspects, the disclosed subject matter relates to compounds having activity as selective HDAC6 inhibitors, methods of making and using the compounds, and compositions comprising the 30 compounds. In certain aspects, the disclosed subject matter relates to compounds having the chemical structure shown in Formulas I or II, in particular Formula I-A, I-B, and I-C, as defined herein. In still further aspects, the disclosed subject matter relates to methods for treating oncological disorders in a patient. For example, disclosed herein are methods whereby an effective amount of a compound or composition disclosed herein is administered to a patient 35 having an oncological disorder, for example melanoma, and who is in need of treatment thereof. 4 WO 2013/134467 PCT/US2013/029521 Methods of using the disclosed compounds to inhibit or kill tumor cells, to inhibit HDAC6, and to augument tumor inflammatory responses are also disclosed. Additional advantages of the disclosed subject matter will be set forth in part in the description that follows and the Figures, and in part will be obvious from the description, or can 5 be learned by practice of the aspects described below. The advantages described below 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. DETAILED DESCRIPTION 10 The materials, compounds, compositions, articles, and methods described herein may be understood more readily by reference to the following detailed description of specific aspects of the disclosed subject matter and the Examples and Figures included therein. Before the present materials, compounds, compositions, and methods are disclosed and described, it is to be understood that the aspects described below are not limited to specific 15 synthetic methods or specific reagents, as such may, of course, vary. 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. Also, throughout this specification, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application 20 in order to more fully describe the state of the art to which the disclosed matter pertains. The references disclosed are also individually and specifically incorporated by reference herein for the material contained in them that is discussed in the sentence in which the reference is relied upon. General Definitions In this specification and in the claims that follow, reference will be made to a number of 25 terms, which shall be defined to have the following meanings: Throughout the description and claims of this specification the word "comprise" and other forms of the word, such as "comprising" and "comprises," means including but not limited to, and is not intended to exclude, for example, other additives, components, integers, or steps. As used in the description and the appended claims, the singular forms "a," "an," and 30 "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a composition" includes mixtures of two or more such compositions, reference to "the compound" includes mixtures of two or more such compounds, reference to "an agent" includes mixture of two or more such agents, and the like. 5 WO 2013/134467 PCT/US2013/029521 "Optional" or "optionally" means that the subsequently described event or circumstance can or cannot occur, and that the description includes instances where the event or circumstance occurs and instances where it does not. Ranges can be expressed herein as from "about" one particular value, and/or to "about" 5 another particular value. When such a range is expressed, another aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent "about," it will be understood that the particular value forms another aspect. 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 10 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. It is also understood that when a value is disclosed, then "less than or equal to" the value, "greater than or equal to the value," and possible ranges between values are also disclosed, as appropriately understood by the skilled 15 artisan. For example, if the value "10" is disclosed, then "less than or equal to 10" as well as "greater than or equal to 10" is also disclosed. It is also understood that throughout the application data are provided in a number of different formats and that this data represent endpoints and starting points and ranges for any combination of the data points. For example, if a particular data point "10" and a particular data point "15" are disclosed, it is understood that 20 greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed. As used herein, by a "subject" is meant an individual. Thus, the "subject" can include 25 domesticated animals (e.g., cats, dogs, etc.), livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), laboratory animals (e.g., mouse, rabbit, rat, guinea pig, etc.), and birds. "Subject" can also include a mammal, such as a primate or a human. By "reduce" or other forms of the word, such as "reducing" or "reduction," is meant lowering of an event or characteristic (e.g., tumor growth). It is understood that this is typically 30 in relation to some standard or expected value, in other words it is relative, but that it is not always necessary for the standard or relative value to be referred to. For example, "reduces tumor growth" means reducing the rate of growth of a tumor relative to a standard or a control. By "prevent" or other forms of the word, such as "preventing" or "prevention," is meant to stop a particular event or characteristic, to stabilize or delay the development or progression of 35 a particular event or characteristic, or to minimize the chances that a particular event or 6 WO 2013/134467 PCT/US2013/029521 characteristic will occur. Prevent does not require comparison to a control as it is typically more absolute than, for example, reduce. As used herein, something could be reduced but not prevented, but something that is reduced could also be prevented. Likewise, something could be prevented but not reduced, but something that is prevented could also be reduced. It is 5 understood that where reduce or prevent are used, unless specifically indicated otherwise, the use of the other word is also expressly disclosed. By "treat" or other forms of the word, such as "treated" or "treatment," is meant to administer a composition or to perform a method in order to reduce, prevent, inhibit, or eliminate a particular characteristic or event (e.g., tumor growth or survival). The term "control" is used 10 synonymously with the term "treat." The term "anticancer" refers to the ability to treat or control cellular proliferation and/or tumor growth at any concentration. It is understood that throughout this specification the identifiers "first" and "second" are used solely to aid in distinguishing the various components and steps of the disclosed subject 15 matter. The identifiers "first" and "second" are not intended to imply any particular order, amount, preference, or importance to the components or steps modified by these terms. Chemical Definitions 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 20 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 25 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. 30 "Z 1 ," "z 2 ," "z 3 ," and "Z 4 " 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. 7 WO 2013/134467 PCT/US2013/029521 The term "aliphatic" as used herein refers to a non-aromatic hydrocarbon group and includes branched and unbranched, alkyl, alkenyl, or alkynyl groups. 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, t 5 butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, dodecyl, tetradecyl, hexadecyl, eicosyl, tetracosyl, and the like. The alkyl group can also be substituted or unsubstituted. The alkyl group can be substituted with one or more groups including, but not limited to, alkyl, halogenated alkyl, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, nitro, silyl, sulfo-oxo, sulfonyl, sulfone, sulfoxide, or thiol, 10 as described below. 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" specifically refers to an alkyl group that is substituted with one or more 15 halide, e.g., fluorine, chlorine, bromine, or iodine. The term "alkoxyalkyl" specifically refers to an alkyl group that is substituted with one or more alkoxy groups, as described below. The term "alkylamino" specifically refers to an alkyl group that is substituted with one or more amino groups, as described below, and the like. When "alkyl" is used in one instance and a specific term such as "alkylalcohol" is used in another, it is not meant to imply that the term "alkyl" does 20 not also refer to specific terms such as "alkylalcohol" and the like. 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 25 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. The term "alkoxy" as used herein is an alkyl group bound through a single, terminal ether 30 linkage; that is, an "alkoxy" group can be defined as -OZ 1 where Z' is alkyl as defined above. 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 (Z 1
Z
2
)C=C(Z
3
Z
4 ) 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 35 explicitly indicated by the bond symbol C=C. The alkenyl group can be substituted with one or 8 WO 2013/134467 PCT/US2013/029521 more groups including, but not limited to, alkyl, halogenated alkyl, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, nitro, silyl, sulfo-oxo, sulfonyl, sulfone, sulfoxide, or thiol, as described below. The term "alkynyl" as used herein is a hydrocarbon group of 2 to 24 carbon atoms with a 5 structural formula containing at least one carbon-carbon triple bond. The alkynyl group can be substituted with one or more groups including, but not limited to, alkyl, halogenated alkyl, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, nitro, silyl, sulfo-oxo, sulfonyl, sulfone, sulfoxide, or thiol, as described below. The term "aryl" as used herein is a group that contains any carbon-based aromatic group 10 including, but not limited to, benzene, naphthalene, phenyl, biphenyl, phenoxybenzene, and the like. The term "heteroaryl" is defined as a group that contains 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. The term "non heteroaryl," which is included in the term "aryl," defines a group that contains an aromatic group 15 that does not contain a heteroatom. The aryl or heteroaryl group can be substituted or unsubstituted. The aryl or heteroaryl group can be substituted with one or more groups including, but not limited to, alkyl, halogenated alkyl, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, nitro, silyl, sulfo-oxo, sulfonyl, sulfone, sulfoxide, or thiol as described herein. The term "biaryl" is a specific type of 20 aryl group and is included in the definition of aryl. Biaryl refers 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. The term "cycloalkyl" 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, 25 cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, etc. The term "heterocycloalkyl" is a cycloalkyl group as defined above where at least one of the carbon atoms of the ring is substituted 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 30 more groups including, but not limited to, alkyl, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, nitro, silyl, sulfo-oxo, sulfonyl, sulfone, sulfoxide, or thiol as described herein. 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 double bound, i.e., C=C. Examples of 35 cycloalkenyl groups include, but are not limited to, cyclopropenyl, cyclobutenyl, cyclopentenyl, 9 WO 2013/134467 PCT/US2013/029521 cyclopentadienyl, cyclohexenyl, cyclohexadienyl, 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 substituted with a heteroatom such as, but not limited to, nitrogen, oxygen, sulfur, or phosphorus. The 5 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, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, aldehyde, amino, carboxylic acid, ester, ether, halide, hydroxy, ketone, nitro, silyl, sulfo-oxo, sulfonyl, sulfone, sulfoxide, or thiol as described herein. 10 The term "cyclic group" is used herein to refer to either aryl groups, non-aryl groups (i.e., cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl groups), or both. Cyclic groups have one or more ring systems that can be substituted or unsubstituted. A cyclic group can contain one or more aryl groups, one or more non-aryl groups, or one or more aryl groups and one or more non-aryl groups. 15 The term "aldehyde" as used herein is represented by the formula -C(O)H. Throughout this specification "C(O)" or "CO" is a short hand notation for C=O, which is also refered to herein as a "carbonyl." The terms "amine" or "amino" as used herein are represented by the formula -NZ Z2 where Z' and Z 2 can each be substitution group as described herein, such as hydrogen, an alkyl, 20 halogenated alkyl, alkenyl, alkynyl, aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group described above. "Amido" is
-C(O)NZZ
2 . The term "carboxylic acid" as used herein is represented by the formula -C(O)OH. A "carboxylate" or "carboxyl" group as used herein is represented by the formula 25 -C(O)O The term "ester" as used herein is represented by the formula -OC(O)Zl or
-C(O)OZ
1 , where Z' can be an alkyl, halogenated alkyl, alkenyl, alkynyl, aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group described above. The term "ether" as used herein is represented by the formula ZIOZ 2 , where Z' and Z 2 30 can be, independently, an alkyl, halogenated alkyl, alkenyl, alkynyl, aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group described above. The term "ketone" as used herein is represented by the formula ZIC(O)Z 2 , where Z' and Z2 can be, independently, an alkyl, halogenated alkyl, alkenyl, alkynyl, aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group described above. 10 WO 2013/134467 PCT/US2013/029521 The term "halide" or "halogen" as used herein refers to the fluorine, chlorine, bromine, and iodine. The term "hydroxyl" as used herein is represented by the formula -OH. The term "nitro" as used herein is represented by the formula -NO 2 . 5 The term "silyl" as used herein is represented by the formula -SiZ 1
Z
2
Z
3 , where Z1, Z2 and Z 3 can be, independently, hydrogen, alkyl, halogenated alkyl, alkoxy, alkenyl, alkynyl, aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group described above. The term "sulfonyl" is used herein to refer to the sulfo-oxo group represented by the 10 formula -S(O) 2 Z , where Z' can be hydrogen, an alkyl, halogenated alkyl, alkenyl, alkynyl, aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group described above. The term "sulfonylamino" or "sulfonamide" as used herein is represented by the formula
-S(O)
2 NH-. 15 The term "thiol" as used herein is represented by the formula -SH. The term "thio" as used herein is represented by the formula -S-.
"R
1 ," "R 2 ," "R 3 ," "R"," etc., where n is some integer, as used herein can, independently, possess one or more of the groups listed above. For example, if R 1 is a straight chain alkyl group, one of the hydrogen atoms of the alkyl group can optionally be substituted with a 20 hydroxyl group, an alkoxy group, an amine 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 (i.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 25 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. 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, diastereomer, and meso compound, and a mixture of isomers, such as a racemic or scalemic 30 mixture. Reference will now be made in detail to specific aspects of the disclosed materials, compounds, compositions, articles, and methods, examples of which are illustrated in the accompanying Examples and Figures. 11 WO 2013/134467 PCT/US2013/029521 Compounds A variety of HDAC6 inhibitors have been investigated (Butler et al., "Rational Design and Simple Chemistry Yield a Superior, Neuroprotective HDAC6 Inhibitor, Tubastatin A," JAm Chem Soc 2010, 132(31):10842-10846; Kalin et al., "Second-Generation Histone Deacetylase 6 5 Inhibitors Enhance the Immunosuppressive Effects of Foxp3+ T-Regulatory Cells," JMed Chem 2012, 55(2):639-65 1). A feature of these agents is the presence of a benzylic linker that is built into a canonical inhibitor, which comprises a "cap-linker-zinc binding group" system. There is a report that discloses HDACi's without the zinc-binding group (ZBG) (Vickers et al., "Discovery of HDAC Inhibitors That Lack an Active Site Zn 2-Binding Functional Group," A CS Med Chem 10 Lett 2012, 3(6):505-508). These agents possessed modest activity against the Class 1 enzymes. The compounds disclosed herein maintain a ZBG, most prefereably a hydroxamic acid group. Futher, the disclosed compounds contain certain urea-based cap groups that are incorporated into a benzyl hydroxamic acid scaffold, leading to potent and selective HDAC6 inhibitors with in vitro anti-melanoma activity. As such, disclosed herein are compounds having 15 Formula I: 0 R1 R2 NHOH AN 0 wherein A is aryl, heteroaryl, or C 1 -Cs alkyl, any of which is optionally substituted with one or more 20 groups chosen from acetyl, C 1
-C
5 alkyl, amino, -NR 6
R
7 , -C(O)NR 6
R
7 , C 1
-C
4 alkoxy, C 1 C 4 alkylhydroxy, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, heteroaryl, halo, hydroxy, thiol, cyano, or nitro; and R and R 2 are independently chosen from hydrogen, C 1 -Cs alkyl, C 1 -Cs alkenyl, C 1 -Cs alkynyl,
C
1 -Cs haloalkyl, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, C 1
-C
3 alkylaryl, aryl, C 1
-C
3 25 alkylheteroaryl, or heteroaryl, any of which is optionally substituted with acetyl, C 1
-C
5 alkyl, amino, -NR 6
R
7 , -C(O)NR 6
R
7 , C 1
-C
4 alkoxy, C 1
-C
4 alkylhydroxy, C 5
-C
6 cycloalkyl,
C
5
-C
6 heterocycloalkyl, aryl, heteroaryl, carbonyl, halo, hydroxy, thiol, cyano, or nitro; or R and R 2 are joined such that together they form an alkylene bridge comprising 2 atoms so that 30 a 5-membered ring is formed with the -NC(O)N- moiety, in which case A is as defined 12 WO 2013/134467 PCT/US2013/029521 above or hydrogen, and which 5-membered ring is optionally substituted with R', R 2 ',
R
1 ", and R 2 ", which are independently, hydrogen, or are CI-Cs alkyl, C 5
-C
6 cycloalkyl,
C
5
-C
6 heterocycloalkyl, CI-C 3 alkylaryl, aryl, CI-C 3 alkylheteroaryl, or heteroaryl any of which is optionally substituted with amino, aryl, C 1
-C
4 alkoxy, halo, or hydroxy; or R' 5 and R 1 " together or R2" and R 2' together form a carbonyl (i.e., =0); or R' and R2' are null and R 1 " and R2" together form a fused phenyl group; and R6 and R 7 are independently H, C 1
-C
4 alkyl, or are joined such that together they form an alkylene bridge comprising 4 or 5 atoms so that a 5 or 6-membered ring is formed with the nitrogen; 10 or a pharmaceutically acceptable salt or hydrate thereof. In some examples, when R 1 and R2 are both hydrogen, A is not hydroxyphenyl. In specific examples, A can be a phenyl, pyridyl, oxazolidyl, or pyrimidyl optionally substituted with C 1
-C
5 alkyl, amino, alkoxy, alkylhydroxy, halo, hydroxy, or thiol. In still other examples, A can be phenyl or phenyl substituted with C 1
-C
5 alkyl, C 1
-C
4 alkoxyl, or halo. In 15 still other example, A can be pyridyl or pyridyl substituted with C 1
-C
5 alkyl, C 1
-C
4 alkoxyl, or halo. In a preferred example, A is phenyl, or methoxyl substituted phenyl, or halo substituted phenyl. In further examples, A can be a phenyl. In still further examples, A can be a phenyl substituted with one or more methoxyl, ethoxyl, or propoxyl groups, for example, A can be a phenyl substituted with one methoxyl group at the ortho-, para-, or meta-position. In a most 20 preferred example, A can be a phenyl substituted with a methoxyl group at the ortho-position. Still further, A can be a phenyl substituted with one or more halo groups, for example, A can be a phenyl with one halo (e.g., Cl, Br, or F) group at the ortho-, para-, or meta-position. In other examples, A can be a phenyl group with one or more carboxylic acids group or an alkyl ester group (e.g., an acetyl group). A can be a C 1 -Cs alkyl group. In still other examples, A can be a 25 phenyl substituted with one or more C 1
-C
4 alkyl groups. A can be a phenyl substituted with one methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, s-butyl, i-butyl group at the ortho-, para-, or meta-position. A can be a phenyl substituted with one or more NH 2 or N(CI-C 4
)
2 groups. In other examples, A can be a n-propyl, i-propyl, n-butyl, t-butyl, s-butyl, i-butyl, n pentyl, i-pentyl, or s-pentyl group. 30 In specific examples, R 1 can be hydrogen, C 1 -Cs alkyl, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with C 1
-C
3 alkyl, amino, -NR 6
R
7 , C 1
-C
4 alkoxy, C 1
-C
4 alkylhydroxy, carbonyl, hydroxy, thiol, or cyano. In specific examples, R 1 can be C 1 -Cs alkyl, for example a C 1
-C
4 alkyl. In other examples, R 1 can be a C 1 -Cs alkyl which is optionally substituted with acetyl, NH 2 , N(C 1
-C
4
)
2
C
1
-C
4 alkoxy, C 1
-C
4 35 C 5
-C
6 heterocycloalkyl, carbonyl, halo, or hydroxy. In preferred examples, R 1 is hydrogen. 13 WO 2013/134467 PCT/US2013/029521 In specific examples, R 2 can be hydrogen, C 1 -Cs alkyl, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with C 1
-C
5 alkyl, amino, -NR 6
R
7 , C 1
-C
4 alkoxy, C 1
-C
4 alkylhydroxy, carbonyl, hydroxy, thiol, or cyano. In specific examples, R 2 can be C 1
-C
5 alkyl, or C 1
-C
5 alkyl substituted with a methoxy, amino, 5 NR 6
R
7 , alkylhydroxy, carbonyl, hydroxy, cyano. In other examples, R 2 can be a C 1
-C
4 alkyl substituted with a heteroaryl, such as imidazole or indole. In other examples R 2 can be a C1-C4 alkyl substituted with a phenyl, hydroxy substituted phenyl, methoxy substited phenyl, halo substituted phenyl, or amino substituted phenyl. In further examples, the disclosed compounds can have Formula I-A 00 R2 NHOH H 10 R, I-A where R2 is as noted herein; each W is independent of the others CH or N; and R 5 is hydrogen,
C
1 -Cs alkyl, C 1 -Cs alkenyl, CI-Cs alkynyl, CI-Cs haloalkyl, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with acetyl, CI-C 5 15 alkyl, amino, -NR 6
R
7 , -C(O)NR 6
R
7 , C 1
-C
4 alkoxy, C 1
-C
4 alkylhydroxy, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, heteroaryl, carbonyl, halo, hydroxy, thiol, cyano, or nitro, or a pharmaceutically acceptable salt or hydrate thereof. In further examples, the disclosed compounds can have Formula I-B R' NHOH H 1% 0
R
5 20 I-B where R 1 is as noted herein; each W is independent of the others CH or N; and R5 is hydrogen, CI-Cs alkyl, C 1 -Cs alkenyl, CI-Cs alkynyl, CI-Cs haloalkyl, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with acetyl, C 1
-C
5 alkyl, amino, -NR 6
R
7 , -C(O)NR 6
R
7 , C 1
-C
4 alkoxy, C 1
-C
4 alkylhydroxy, C 5
-C
6 cycloalkyl, C 5
-C
6 14 WO 2013/134467 PCT/US2013/029521 heterocycloalkyl, aryl, heteroaryl, carbonyl, halo, hydroxy, thiol, cyano, or nitro, or a pharmaceutically acceptable salt or hydrate thereof. The disclosed compounds can be selective HDAC6i's. A homology model (Butler et al., JAm Chem Soc 2010, 132(31):10842-10846) shows the entrance to the binding site is wider and 5 shallower for HDAC6 than that of HDAC 1. This model also shows a lipophillic cavity. As such, the disclosed compounds can contain cetain branched-elements incorporated into the aryl urea cap group, primarily at A, R 1 and/or R 2 , to enhance both the potency and selectivity by accessing this side cavity and leading to better interactions with the surface of HDAC6. Accessing this side cavity can be, in one aspect, accomplished through substituting the 10 proximal nitrogen atom of the urea linker relative to the benzyl linker, i.e., R2 in Formula I. The synthesis of these branched acyclic ureas is accomplished as outlined in Scheme 1. As an example, a variety of amines undergo reductive amination with methyl 4-formylbenzoate 2 to form the desired secondary amines 3a-h. Subsequent reaction of 3a-h with the approprate isocyanates affords the branched urea esters 4a-h. Aryl isocyanates are shown in Scheme 1; 15 however, other isocyanates can be used to vary the "A" group in Formula I (e.g., heteroaryl, or alkyl). This chemistry generates a series of ureas displaying branched substitutions on the nitrogen proximal to the benzylic linker (R 2 ). The hydroxamic acid group is installed using hydroxylamine under basic conditions to provide the hydroxamic acids 5a-h. 15 WO 2013/134467 PCT/US2013/029521 Scheme 1: Synthesis of proximal N-substituted hydroxamic acids 0 'N OH OMeH H H N YNH - 0 0 0 0 a R2 b 1 H R I oH -HN "N~ - 0 2 3a-h 4a-g Z = -OCH 3 R -0 O e 5a-g Z = -NHOH RH2 OH OH b c d R10= -H R2 e f g h Reagents and conditions: (a) R 2
-NH
2 , NaCNBH 3 , rt, 5% AcOH/DCM, 16 h; (b) Aryl-NCO, DCM, rt, 16 h; (c) 50% wt NH 2 OH, NaOH, THF/MeOH (1:1), 0 'C to rt, 30 min. 5 Accessing this side cavity can be, in another aspect, accomplished through substituting the distal nitrogen atom of the urea linker relative to the benzyl linker, i.e., R 1 in Formula I. The synthesis of these branched acyclic ureas is accomplished as outlined in Scheme 2. As an example, a copper-mediated Buchwald coupling reaction is used in order to assemble anilines 10 6a-b from iodobenzene, as these intermediates are not commercially available (Kwong et al., "Copper-catalyzed coupling of alkylamines and aryl iodides: An efficient system even in an air atmosphere" Org Lett 2002, 4(4):581-584). Triphosgene chemistry is implemented to convert methyl 4-(aminomethyl)benzoate into the corresponding isocyanate, which undergoes reaction with seconday amines 6a-c to afford the penultimate esters 7a-c. Final conversion to the 15 hydroxamic acids is accomplished as in Scheme I to complete the synthesis of 8a-c. 16 WO 2013/134467 PCT/US2013/029521 Scheme 2: Synthesis of distal N-substituted hydroxamic acids 0 R1 R1 HZ NN N c 7a-c Z = -OCH 3 bLII 6a-b Ba-c Z = -NHOH V- \ O a b C Reagents and conditions: (a) R 1
-NH
2 , Cul, K 3 P0 4 , ethylene glycol, iPrOH, 80 'C, 18 h; (b) i. triphosgene, sat. aq bicarbonate/DCM (1:1), 0 'C, 30 min; ii. methyl 4-(aminomethyl)benzoate 5 HCl, Et 3 N, DCM, rt, 16 h; (c) 50% wt NH 2 OH, NaOH, THF/MeOH (1:1), 0 'C to rt, 30 min. Specific compounds according to Formula I are as follows. 0 0O N OH 5a0 H H OH NYN0 H I H (t 5a HO 0 HN O Il OH O d r N H 5b N0 N OH e SH H It 0 5b ~ N N 0 5c OH OOH O H OH N OH 5dN YN 5 N YN e- H 5e I 0 5d 00 0 OOH OH H ~ NH H I H Y 5f N 5g 17 WO 2013/134467 PCT/US2013/029521 H. NOH SOH N MO OHM Br OH H-O N NN 11N :yN0 8a Cr 0 5h 0 0 H OH N NN N NN NN OH O Y N,,e 08c 8b 0 0 N' OH N'OH N N HN~ N N F
H
3 00 9a 9 O 0 N. NjOH N O N N H NN I He F 9c Br .) O 0 H IH HH F, "_e N , F O 0 A) OH N NOH 00 N NOH N' NOH I H HH NN N N _e N 0 or pharmaceutically acceptable salts or hydrates thereof. 18 WO 2013/134467 PCT/US2013/029521 Accessing the side cavity of HDAC6 can also be, in still another aspect, accomplished through linking the distal and proximal nitrogen atoms of the urea linker via an alkylene bridge, i.e., joining R 1 and R 2 together to form a 5-membered ring with the -NC(O)N- moiety in Formula I. Thus, in further examples the disclosed compounds can have 5 Formula I-C A 0 I-C wherein A is hydrogen, or A is aryl, heteroaryl, or C 1 -Cs alkyl, any of which is optionally substituted 10 with one or more groups chosen from acetyl, C 1
-C
5 alkyl, amino, -NR 6
R
7 , -C(O)NR 6 R ,
C
1
-C
4 alkoxy, C 1
-C
4 alkylhydroxy, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, aryl, heteroaryl, halo, hydroxy, thiol, cyano, or nitro, with R 6 and R 7 as defined above; and RI', R 2 ', Rl", and R 2 ", are independently, hydrogen, or are CI-Cs alkyl, C 5
-C
6 cycloalkyl, C 5
-C
6 heterocycloalkyl, C 1
-C
3 alkylaryl, aryl, CI-C 3 alkylheteroaryl, or heteroaryl any of which 15 is optionally substituted with amino, aryl, C 1
-C
4 alkoxy, halo, or hydroxy; or R' and Rl" together or R2" and R 2 ' together form a carbonyl (i.e., =0); or R' and R2' are null and
R
1 " and R2" together form a fused phenyl group. In certain examples, R 2 ' and R 2 " are both methyl. In other examples R 2 ' is hydrogen and R2" is methyl, ethyl, propyl, i-propyl, n-butyl, i-butyl, benzyl, tosyl, hydroxyphenyl, C 1
-C
4 20 alkoxyphenyl, or aminophenyl. In other examples R2' and R2" form a carboxyl (i.e., =0) group, or a pharmaceutically acceptable salt or hydrate thereof. In certain examples, R' and Rl" are both methyl. In other examples R' is hydrogen and Rl" is methyl, ethyl, propyl, i-propyl, n-butyl, i-butyl, benzyl, tosyl, hydroxyphenyl, C 1
-C
4 alkoxyphenyl, or aminophenyl. In other examples R' and R 1 " form a carboxyl (i.e., =0) group. 25 The synthesis of these cyclic ureas is accomplished as outlined in Scheme 3. 19 WO 2013/134467 PCT/US2013/029521 Scheme 3: Synthesis of cyclic urea hydroxamic acids 0 R2 00 0 0CH R1~ NCONH O~ N OH
H
3
CO
2 C
NH
2 R/R N R2 00 00 0 NHOH N R1N 0 OCH 0
OCH
3 d R1 OCH3 H N N HN HO'j R1 0 Reagents and conditions: (a) i. aq NaOH, ii. H+ 60'C lh; (b) KOtBu, DMF, 0 0 C-RT; (c) aq
NH
2 OH, NaOH, THF/MeOH; (d) triphosgene, Et 3 N. 5 Specific examples of compounds of Formula I-C are as follows. OH OH H ~ N, O 10a O1 0b 0 0 0 NOH N N OH HNN HN 4 O 11a HO HO 0 0 0 0 -N N' OH OH H H 0 0 or pharmaceutically acceptable salts or hydrates thereof. 20 WO 2013/134467 PCT/US2013/029521 The disclosed compounds comprise, in one aspect, branched aryl or alkyl urea cap groups, or cyclic urea cap groups, introduced into the canonical HDACi platform. Introduction of branching elements, particularly to the proximal nitrogen atom of the urea motif, has led to 5 the discovery of potent inhibitors that show excellent selectivity for HDAC6 versus the full panel of HDACs and are capable of inducing selective hyperacetylation of a-tubulin compared to histone protein. The SAR developed to this point indicates the branched urea scaffold imparts substantial gains in the desired biochemical activity. These compounds were also screened in cell systems, and both 5g and 5h were found to be capable of inhibiting the growth of B 16 10 melanoma cell line. Also disclosed are hydroxamate compounds that are devoid of the urea motif. Such compounds have Formula II. /0 R 2 NHOH
R
8 II 15 wherein R2 is as defined above and R8 is acetyl, C 1
-C
5 alkyloxycarbonyl, carbobenzyloxy, methoxybenzyl carbonyl, benzoyl, benzyl, methoxybenzyl, dimethoxybenzyl, methoxyphenyl,
C
1
-C
5 alkylcarbamate, or aryl sulfonyl, i.e., R9(S0 2 ), where R 9 is aryl optionally substituted with
C
1
-C
5 alkyl, amino, methoxyl, halo, or hydroxy, or a pharmaceutically acceptable salt or hydrate thereof. In preferred examples, R 8 can be C 1
-C
5 alkyloxycarbonyl or arylsulfonyl. Specific 20 examples of compounds of Formula II are as follows. 0 N OH NOH 0 H or0 N Hr 00N"e 0 0 ONNOH O NNOH or pharmaceutically acceptable salts or hydrates thereof. 21 WO 2013/134467 PCT/US2013/029521 Also disclosed herein are pharmaceutically-acceptable salts and hydrates of the disclosed compounds. Pharmaceutically-acceptable salts include salts of the disclosed compounds that are prepared with acids or bases, depending on the particular substituents found on the compounds. Under conditions where the compounds disclosed herein are sufficiently basic or acidic to form 5 stable nontoxic acid or base salts, administration of the compounds as salts can be appropriate. Examples of pharmaceutically-acceptable base addition salts include sodium, potassium, calcium, ammonium, or magnesium salt. Examples of physiologically-acceptable acid addition salts include hydrochloric, hydrobromic, nitric, phosphoric, carbonic, sulphuric, and organic acids like acetic, propionic, benzoic, succinic, fumaric, mandelic, oxalic, citric, tartaric, malonic, 10 ascorbic, alpha-ketoglutaric, alpha-glycophosphoric, maleic, tosyl acid, methanesulfonic, and the like. Thus, disclosed herein are the hydrochloride, nitrate, phosphate, carbonate, bicarbonate, sulfate, acetate, propionate, benzoate, succinate, fumarate, mandelate, oxalate, citrate, tartarate, malonate, ascorbate, alpha-ketoglutarate, alpha-glycophosphate, maleate, tosylate, and mesylate salts. Pharmaceutically acceptable salts of a compound can be obtained using standard 15 procedures well known in the art, for example, by reacting a sufficiently basic compound such as an amine with a suitable acid affording a physiologically acceptable anion. Alkali metal (for example, sodium, potassium or lithium) or alkaline earth metal (for example calcium) salts of carboxylic acids can also be made. Methods of Use 20 Further provided herein are methods of treating or preventing cancer in a subject, comprising administering to the subject an effective amount of a compound or composition as disclosed herein. Additionally, the method can further comprise administering an effective amount of ionizing radiation to the subject. Methods of killing a tumor cell are also provided herein. The methods comprise 25 contacting a tumor cell with an effective amount of a compound or composition as disclosed herein. The methods can further include administering a second compound or composition (e.g., an anticancer agent) or administering an effective amount of ionizing radiation to the subject. Also provided herein are methods of radiotherapy of tumors, comprising contacting the tumor with an effective amount of a compound or composition as disclosed herein and 30 irradiating the tumor with an effective amount of ionizing radiation. Methods of treating inflammation in a subject are further provided herein, the methods comprising administering to the subject an effective amount of a compound or composition as described herein. Optionally, the methods can further include administering a second compound or composition (e.g., an anti inflammatory agent). 22 WO 2013/134467 PCT/US2013/029521 The disclosed subject matter also concerns methods for treating a subject having an oncological disorder or condition. In one embodiment, an effective amount of one or more compounds or compositions disclosed herein is administered to a subject having an oncological disorder and who is in need of treatment thereof. The disclosed methods can optionally include 5 identifying a subject who is or can be in need of treatment of an oncological disorder. The subject can be a human or other mammal, such as a primate (monkey, chimpanzee, ape, etc.), dog, cat, cow, pig, or horse, or other animals having an oncological disorder. Means for administering and formulating compounds for administration to a subject are known in the art, examples of which are described herein. Oncological disorders include, but are not limited to, 10 cancer and/or tumors of the anus, bile duct, bladder, bone, bone marrow, bowel (including colon and rectum), breast, eye, gall bladder, kidney, mouth, larynx, esophagus, stomach, testis, cervix, head, neck, ovary, lung, mesothelioma, neuroendocrine, penis, skin, spinal cord, thyroid, vagina, vulva, uterus, liver, muscle, pancreas, prostate, blood cells (including lymphocytes and other immune system cells), and brain. Specific cancers contemplated for treatment include 15 carcinomas, Karposi's sarcoma, melanoma, mesothelioma, soft tissue sarcoma, pancreatic cancer, lung cancer, leukemia (acute lymphoblastic, acute myeloid, chronic lymphocytic, chronic myeloid, and other), and lymphoma (Hodgkin's and non-Hodgkin's), and multiple myeloma. Other examples of cancers that can be treated according to the methods disclosed herein are adrenocortical carcinoma, adrenocortical carcinoma, cerebellar astrocytoma, basal cell 20 carcinoma, bile duct cancer, bladder cancer, bone cancer, brain tumor, breast cancer, Burkitt's lymphoma, carcinoid tumor, central nervous system lymphoma, cervical cancer, chronic myeloproliferative disorders, colon cancer, cutaneous T-cell lymphoma, endometrial cancer, ependymoma, esophageal cancer, gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, germ cell tumor, glioma,, hairy cell leukemia, head and neck cancer, 25 hepatocellular (liver) cancer, hypopharyngeal cancer, hypothalamic and visual pathway glioma, intraocular melanoma, retinoblastoma, islet cell carcinoma (endocrine pancreas), laryngeal cancer, lip and oral cavity cancer, liver cancer, medulloblastoma, Merkel cell carcinoma, squamous neck cancer with occult mycosis fungoides, myelodysplastic syndromes, myelogenous leukemia, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, non 30 small cell lungcancer, oral cancer, oropharyngeal cancer, osteosarcoma, ovarian cancer, pancreatic cancer, paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pheochromocytoma, pineoblastoma and supratentorial primitive neuroectodermal tumor, pituitary tumor, plasma cell neoplasm/multiple myeloma, pleuropulmonary blastoma, prostate cancer, rectal cancer, renal cell (kidney) cancer, retinoblastoma, rhabdomyosarcoma, salivary 35 gland cancer, Ewing's sarcoma, soft tissue sarcoma, Sezary syndrome, skin cancer, small cell 23 WO 2013/134467 PCT/US2013/029521 lung cancer, small intestine cancer, supratentorial primitive neuroectodermal tumors, testicular cancer, thymic carcinoma, thymoma, thyroid cancer, transitional cell cancer of the renal pelvis and ureter, trophoblastic tumor, urethral cancer, uterine cancer, vaginal cancer, vulvar cancer, Waldenstr6m's macroglobulinemia, and Wilms' tumor. 5 Melanoma and mantle cell lymphoma In a preferred embodiment, disclosed herein is a method of treating a subject with melanoma by administering an effective amount of a compound of Formula 1 or II. Melanoma is currently the fastest growing cancer in incidence according to the World Health Organization. Currently, few therapies provide significant prolongation of survival for metastatic melanoma. 10 Immunotherapy is an attractive modality with potentially few side effects due to the antigen specificity of adaptive immunity. The latest therapy approved by the FDA for the treatment of melanoma was ipilimumab, an antibody against CTLA-4, a key regulator of T-cell activity; however, this therapy offers modest improvements in overall survival. Overcoming mechanisms of tumor-mediated immune suppression requires targeting 15 multiple pathways. One strategy that has gained attention has been the use of histone deacetylase inhibitors (HDACi). Indeed, HDACi treatment has been shown to augment the expression of immunologically relevant genes such as MHC and co-stimulatory molecules. Inhibition of IL-10 is a potent anti-inflammatory cytokine upon treatment of macrophages with an HDACi. However; most studies to date have used pan-HDACi, which inhibit all 11 zinc 20 dependent HDACs. Therefore, the use of more selective HDACi is preferable in order to minimize side effects. As demonstrated herein, HDAC6 is a molecular target in at least melanoma. Both pharmacologic and genetic disruption of HDAC6 in B16 murine melanoma cells' using HDAC6-selective inhibitors (HDAC6i) and targeted shRNA (HDAC6KD), respectively, led to 25 inhibition of proliferation, characterized by G 1 arrest measured by propidium iodine staining for DNA content. Furthermore, treatment with the HDAC6i led to enhanced expression of immunologically relevant receptors including MHC-I and MHC-II. In vivo, subcutaneous injection in wild type mice of HDAC6KD B16 cells led to delayed tumor growth as compared with control cells. However, this effect was abrogated in experiments using SCID mice, which 30 lack T- and B-cells, suggesting a critical immune component for tumor control in vivo. The mechanism(s) by which HDAC6 regulates tumor immunogenicity are yet to be defined. One possible mechanism arises from protein immunoprecipitation studies which demonstrate that HDAC6 interacts with, and potentially regulates of STAT3, an important survival and pathogenic factor in melanoma, which also has implications for immune tolerance. 24 WO 2013/134467 PCT/US2013/029521 The expression HDAC6 was found to be upregulated in a majority of melanoma patient tumor biopsies by gene microarray analysis, as compared with normal skin. This observation was supported by immunohistochemically-stained patient melanoma tissue microarray. Taken together, HDAC6 inhibition is an attractive therapeutic target in melanoma and 5 mantle cell lymphoma by both delaying tumor growth and conferring a more attractive immune target, providing rationale for the development and use of selective HDAC6i. Inflammamatory responses It has previously been shown that tumor antigen specific CD8+ T cells are unresponsive in patients with melanoma (Lee et al., Nat. Med. 1999, 5:677-85). T cells infiltrating the bone 10 marrow of patients with multiple myeloma are also unresponsive (Noonan et al. Cancer Res. 65:2026-34, 2005). The conclusion of these studies, along with several other reports in the literature, is that CD4+ T cells are rendered tolerant to tumor antigens early in tumor progression. This presents a significant barrier to the development of effective cancer immunotherapy. 15 The role of histone deacetylases (HDACs) in the epigenetic regulation of inflammatory responses in APCs is disclosed herein. HDACs are a group of enzymes that remove an acetyl group from lysine residues on histones to regulate chromatin architecture and gene expression. HDACs are grouped into four distinct classes as depicted in Figure 1. HDACs are targets for histone deacetylase inhibitors (HDACi) as depicted in Figure 2. 20 HDACi's are structurally diverse compounds that are capable of targeting several HDACs. HDACi's induce differentiation, cell cycle and growth arrest in cancer cells. There is an emerging role for HDACi's as modulators of inflammation and antitumor responses. It was previously found that Pan-HDACi LAQ824 augments inflammatory responses in macrophages through transcriptional regulation of IL-10. Pan-HDACI LAQ824 was also found 25 to restore the responsiveness of tolerant T cells (Wang et al. Jlmmunol 2011, 186:3986-96). The mechanisms and relevant targets of Pan-HDACIs are difficult to elucidate given their multiple effects. Understanding the expression and function of specific HDACs in APCs may unveil novel targets to influence immune activation versus immune tolerance. The identified target(s) may then be subject to pharmacologic inhibition with isotype-selective HDACi's. 30 HDAC6 was found to influence the IL-10 gene expression in APCs as shown in Figure 3. HDAC6 is a 13 1kDa protein encoded on the X chromosome that is mainly cytoplasmic; however, recent data suggests that HDAC6 may also be present in the nucleus). HDAC6 has tubulin deacetylase activity related to cell motility and T cell/APC synapse. There are isotype selective HDAC6 inhibitors available. Figure 4 illustrates the genetic or pharmacologic 35 disruption of HDAC6 inhibits IL-10. Figure 5 illustrates the genetic disruption of HDAC6 25 WO 2013/134467 PCT/US2013/029521 enhances APC function. Mechanisms as shown by CHIP analysis of IL-I0 gene promotor in macrophages include H3 and H4 acetylation; HDAC6 recruitment; and binding of STAT3 and other transcription factors at several timepoints after LPS stimulation as shown in Figure 6. Figure 7 illustrates that knocking down HDAC6 results in a decreased recruitment of the 5 transcriptional activator STAT3 to the IL-10 gene promotor. The C-terminus of HDAC6 is required for interaction with HDAC 11. Figure 8 illustrates that disruption of STAT3 binding to the gene promotor resulted in decreased recruitment of HDAC6 and diminished IL-10 production. Figure 9 illustrates that the disruption of HDAC6 inhibits STAT3 phosphorylation. Figure 10 illustrates that there is increased expression of HDAC6 and IL-I OmRNA in 10 human melanoma. Figure 11 is a series of images that illustrate HDAC6 expression in murine and human melanoma cell lines. Figure 12 is a series of images depicting HDAC protein expression in melanoma. Figure 13 is a series of images depicting decreased proliferation and cell cycle arrest in melanoma cells lacking HDAC6. Figure 14 is a series of images depicting melanoma cells lacking in HDAC6 are more immunogenic. 15 As shown in Figure 14A and 14B, B16 cells treated with the HDAC6i ST-2-92 displayed an elevated expression of MHC-I and -II molecules relative to untreated B16 cells. Similar changes in MHC expression were observed in B 16 cells in which HDAC6 was knocked down. Of note, a delay in tumor growth was observed in C57BL16 mice challenged in vivo with B16 KDHDAC6 cells (Figure 14C). This delay in tumor growth in KDHDAC6 melanoma cells 20 could be a reflection of their diminished proliferation (FigureS 12-13) and/or an increase in their immunogenicity leading to improved immune recognition and clearance. To address this question, C57BL16 SCID mice were challenged with either KDHDAC6 or WTB16 melanoma cells. Unlike immune competent mice in which a delay in KDHDAC6 tumor growth was observed (Figure 14C); such an effect was not observed in SCID mice challenged with the same 25 KDHDAC6 cells (Figure 14D). These results suggest that the immunological effects triggered by disruption of HDAC6 in melanoma cells make these cells "better seen" by the immune system. Figure 15 is a series of images depicting the pharmacologic inhibition of HDAC6 in melanoma cells resulted in cell cycle arrest and increased expression of MHC molecules. It was 30 also found that melanoma cells treated with HDAC6 specific inhibitors are better activators of T cells (CD4 and/or CD8). The procedures for this finding include loading OVA-peptide into melanoma cells (treated or not with Tubastatin A) and adding OT -lor OT -II transgenic T -cells (naive or tolerized) and determining their production of IL-2 and IFN-gamma. Figure 16 is an image depicting Tubastatin-A inhibits JAK2/STAT3 phosphorylation in 35 B16 murine melanoma cells in vivo. Figure 17 is a series of images depicting Tubastatin A 26 WO 2013/134467 PCT/US2013/029521 augments antigen-specific CD4+ T-cell responses to vaccination in melanoma bearing mice. There is an anti-melanoma effect after administration of tubastatin A in vivo (alone or in combination with anti-CLTA4). Figure 18 illustrates the Tubastatin A, a selective HDAC6 inhibitor decreased STAT3 5 phosphorylation and recruitment to the IL-10 gene promotor in APCs. Figure 19 illustrates the phenotypic and functional changes in APCs treated with Tubastatin A. Figure 20 illustrates that tubastatin A-treated APCs are better activators of naive T cells and restore the responsiveness of anergic T cells. Figure 21 is a graph depicting the antitumor effect of Tubastatin A in vivo. Figure 22 depicts that Tubastatin A does not affect PEM. Figure 23 is a series of images 10 depicting the immunological effects of Tubastatin A upon macrophages. Figure 24 is a series of images depicting Tubastatin A inhibits IL-10 transcription by disrupting the JAKISTAT3 pathway in macrophages. Figure 25 is a graph depicting the inhibitory effect of Tubastatin A upon IL-10 production is lost in the absence of HDAC6. Figure 26 is a flow chart depicting the experimental design of the in vitro antigen-presenting studies. Figure 27 is a series of images 15 depicting that Tubastatin A treated macrophages are better activators of naIve Tcells and restore function of anergic T-cells. Figure 28 is a series of images depicting in vivo treatment with tubastatin A augment the response of antigen-specific T-cell to vaccination. The experiments with Tubastatin A in APCs above indicate that treatment of macrophages with Tubastatin-A increased the expression of co-stimulatory molecules and 20 inhibits IL-10 production by these cells. Tubastatin A-treated macrophages are better activators of naIve T-cells and restore the responsiveness of anergic T -cells in vitro. In vivo treatment with Tubastatin-A enhances antigen-specific T-cell responses to vaccination. Mechanistically, Tubastatin-A disrupt JAKISTAT3/IL-iO pathway and tip the balance towards immunogenic rather than tolerogenic macrophages. 25 Figure 29 is an image depicting HDAC6 expression in human MCL. Figure 30 is a series of images depicting the disruption of HDAC6 in human MCL cell lines. Figure 31 is an image depicting the disruption of HDAC6 in murine FC-muMCLI cells. Figure 32 is an image depicting the immunological effects of HDAC6 inhibition in MCL. Changes in MHC, costimulatory molecules and/or cytokine production in response to LPS or CpG +/- ST-3- 06 or 30 Tubastatin A are show. Figure 33 is a series of images depicting the antigenpresenting function of FC-muMCLI cells treated with ST-3-06. Figure 34 is a series of images depicting the antigen-presenting function of FC-muMCLI cells treated with Tubastatin A. Figure 35 is an image depicting the antitumor effect of tubastatin A in vivo. The data showed that HDAC6 inhibition augments the immunogenicity of MCL cells. HDAC6 is required for STAT3 35 activation in APCs and STAT3 diminishes the immunogenicity of tumor cells. 27 WO 2013/134467 PCT/US2013/029521 Figure 36 is a series of images depicting the disruption of HDAC6 inhibits STAT3 phosphorylation in APCs. The C-terminus of HDAC6 is required for interaction with HDAC 11. (A) Constructs of HDAC6 coding for different lengths of the proteins and carrying the FLAG epitope. (B) HDAC6 constructs were over-expressed in HeLa cells and their expression was 5 evaluated by western blot using an anti-FLAG antibody or (C) immunoprecipatated to evaluate their interaction with HDAC 11. Figure 37 is a series of images depicting ST-3-06 decreased STAT3 phosphorylation and recruitment to the IL-10 gene promotor in APCs. Human MCL cells display an enhanced expression of HDAC6. Disruption of HDAC6 in malignant B-cells inhibits their proliferation 10 and is associated with induction of apoptosis. Pharmacologic or genetic disruption of HDAC6 in MCL cells augment their antigen-presenting capabilities leading to better T-cell activation and restoration of function of anergic Tcells in vitro. In vivo treatment of MCL-bearing mice with Tubastatin-A is associated with a strong antitumor effect. Mechanistically, is has been have found that HDAC6 interacts with STAT3 in APCs. Disclosed herein is the rationale to use 15 HDAC6 specific inhibitor(s) alone or in combination with STAT3 inhibitors in MCL. Compositions, Formulations and Methods of Administration In vivo application of the disclosed compounds, and compositions containing them, can be accomplished by any suitable method and technique presently or prospectively known to those skilled in the art. For example, the disclosed compounds can be formulated in a 20 physiologically- or pharmaceutically-acceptable form and administered by any suitable route known in the art including, for example, oral, nasal, rectal, topical, and parenteral routes of administration. As used herein, the term parenteral includes subcutaneous, intradermal, intravenous, intramuscular, intraperitoneal, and intrasternal administration, such as by injection. Administration of the disclosed compounds or compositions can be a single administration, or at 25 continuous or distinct intervals as can be readily determined by a person skilled in the art. The compounds disclosed herein, and compositions comprising them, can also be administered utilizing liposome technology, slow release capsules, implantable pumps, and biodegradable containers. These delivery methods can, advantageously, provide a uniform dosage over an extended period of time. The compounds can also be administered in their salt 30 derivative forms or crystalline forms. The compounds disclosed herein can be formulated according to known methods for preparing pharmaceutically acceptable compositions. Formulations are described in detail in a number of sources which are well known and readily available to those skilled in the art. For example, Remington's Pharmaceutical Science by E.W. Martin (1995) describes formulations 35 that can be used in connection with the disclosed methods. In general, the compounds disclosed 28 WO 2013/134467 PCT/US2013/029521 herein can be formulated such that an effective amount of the compound is combined with a suitable carrier in order to facilitate effective administration of the compound. The compositions used can also be in a variety of forms. These include, for example, solid, semi-solid, and liquid dosage forms, such as tablets, pills, powders, liquid solutions or suspension, suppositories, 5 injectable and infusible solutions, and sprays. The preferred form depends on the intended mode of administration and therapeutic application. The compositions also preferably include conventional pharmaceutically-acceptable carriers and diluents which are known to those skilled in the art. Examples of carriers or diluents for use with the compounds include ethanol, dimethyl sulfoxide, glycerol, alumina, starch, saline, and equivalent carriers and diluents. To provide for 10 the administration of such dosages for the desired therapeutic treatment, compositions disclosed herein can advantageously comprise between about 0.1% and 99%, and especially, 1 and 150% by weight of the total of one or more of the subject compounds based on the weight of the total composition including carrier or diluent. Formulations suitable for administration include, for example, aqueous sterile injection 15 solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient; and aqueous and nonaqueous sterile suspensions, which can include suspending agents and thickening agents. The formulations can be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and can be stored in a freeze dried lyophilizedd) condition requiring only the 20 condition of the sterile liquid carrier, for example, water for injections, prior to use. Extemporaneous injection solutions and suspensions can be prepared from sterile powder, granules, tablets, etc. It should be understood that in addition to the ingredients particularly mentioned above, the compositions disclosed herein can include other agents conventional in the art having regard to the type of formulation in question. 25 Compounds disclosed herein, and compositions comprising them, can be delivered to a cell either through direct contact with the cell or via a carrier means. Carrier means for delivering compounds and compositions to cells are known in the art and include, for example, encapsulating the composition in a liposome moiety. Another means for delivery of compounds and compositions disclosed herein to a cell comprises attaching the compounds to a protein or 30 nucleic acid that is targeted for delivery to the target cell. U.S. Patent No. 6,960,648 and U.S. Application Publication Nos. 20030032594 and 20020120100 disclose amino acid sequences that can be coupled to another composition and that allows the composition to be translocated across biological membranes. U.S. Application Publiation No. 20020035243 also describes compositions for transporting biological moieties across cell membranes for intracellular 35 delivery. Compounds can also be incorporated into polymers, examples of which include poly 29 WO 2013/134467 PCT/US2013/029521 (D-L lactide-co-glycolide) polymer for intracranial tumors; poly[bis(p-carboxyphenoxy) propane:sebacic acid] in a 20:80 molar ratio (as used in GLIADEL); chondroitin; chitin; and chitosan. For the treatment of oncological disorders, the compounds disclosed herein can be 5 administered to a patient in need of treatment in combination with other antitumor or anticancer substances and/or with radiation and/or photodynamic therapy and/or with surgical treatment to remove a tumor. These other substances or treatments can be given at the same as or at different times from the compounds disclosed herein. For example, the compounds disclosed herein can be used in combination with mitotic inhibitors such as taxol or vinblastine, alkylating agents 10 such as cyclophosamide or ifosfamide, antimetabolites such as 5-fluorouracil or hydroxyurea, DNA intercalators such as adriamycin or bleomycin, topoisomerase inhibitors such as etoposide or camptothecin, antiangiogenic agents such as angiostatin, antiestrogens such as tamoxifen, and/or other anti-cancer drugs or antibodies, such as, for example, GLEEVEC (Novartis Pharmaceuticals Corporation) and HERCEPTIN (Genentech, Inc.), respectively, or an 15 immunotherapeutic such as ipilimumab and bortezomib. In other aspect, the disclosed compounds are coadministered with other HDAC inhibitors like ACY-1215, Tubacin, Tubastatin A, ST-3-06, OR ST-2-92. In certain examples, compounds and compositions disclosed herein can be locally administered at one or more anatomical sites, such as sites of unwanted cell growth (such as a 20 tumor site or benign skin growth, e.g., injected or topically applied to the tumor or skin growth), optionally in combination with a pharmaceutically acceptable carrier such as an inert diluent. Compounds and compositions disclosed herein can be systemically administered, such as intravenously or orally, optionally in combination with a pharmaceutically acceptable carrier such as an inert diluent, or an assimilable edible carrier for oral delivery. They can be enclosed 25 in hard or soft shell gelatin capsules, can be compressed into tablets, or can be incorporated directly with the food of the patient's diet. For oral therapeutic administration, the active compound can be combined with one or more excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, aerosol sprays, and the like. 30 The tablets, troches, pills, capsules, and the like can also contain the following: binders such as gum tragacanth, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such as sucrose, fructose, lactose or aspartame or a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring can be added. 35 When the unit dosage form is a capsule, it can contain, in addition to materials of the above type, 30 WO 2013/134467 PCT/US2013/029521 a liquid carrier, such as a vegetable oil or a polyethylene glycol. Various other materials can be present as coatings or to otherwise modify the physical form of the solid unit dosage form. For instance, tablets, pills, or capsules can be coated with gelatin, wax, shellac, or sugar and the like. A syrup or elixir can contain the active compound, sucrose or fructose as a sweetening agent, 5 methyl and propylparabens as preservatives, a dye and flavoring such as cherry or orange flavor. Of course, any material used in preparing any unit dosage form should be pharmaceutically acceptable and substantially non-toxic in the amounts employed. In addition, the active compound can be incorporated into sustained-release preparations and devices. Compounds and compositions disclosed herein, including pharmaceutically acceptable 10 salts, or hydrates thereof, can be administered intravenously, intramuscularly, or intraperitoneally by infusion or injection. Solutions of the active agent or its salts can be prepared in water, optionally mixed with a nontoxic surfactant. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, triacetin, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations can contain a preservative to prevent 15 the growth of microorganisms. The pharmaceutical dosage forms suitable for injection or infusion can include sterile aqueous solutions or dispersions or sterile powders comprising the active ingredient, which are adapted for the extemporaneous preparation of sterile injectable or infusible solutions or dispersions, optionally encapsulated in liposomes. The ultimate dosage form should be sterile, 20 fluid and stable under the conditions of manufacture and storage. The liquid carrier or vehicle can be a solvent or liquid dispersion medium comprising, for example, water, ethanol, a polyol (for example, glycerol, propylene glycol, liquid polyethylene glycols, and the like), vegetable oils, nontoxic glyceryl esters, and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the formation of liposomes, by the maintenance of the required 25 particle size in the case of dispersions or by the use of surfactants. Optionally, the prevention of the action of microorganisms can be brought about by various other antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, buffers or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by 30 the inclusion of agents that delay absorption, for example, aluminum monostearate and gelatin. Sterile injectable solutions are prepared by incorporating a compound and/or agent disclosed herein in the required amount in the appropriate solvent with various other ingredients enumerated above, as required, followed by filter sterilization. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum 31 WO 2013/134467 PCT/US2013/029521 drying and the freeze drying techniques, which yield a powder of the active ingredient plus any additional desired ingredient present in the previously sterile-filtered solutions. For topical administration, compounds and agents disclosed herein can be applied in as a liquid or solid. However, it will generally be desirable to administer them topically to the skin as 5 compositions, in combination with a dermatologically acceptable carrier, which can be a solid or a liquid. Compounds and agents and compositions disclosed herein can be applied topically to a subject's skin to reduce the size (and can include complete removal) of malignant or benign growths, or to treat an infection site. Compounds and agents disclosed herein can be applied directly to the growth or infection site. Preferably, the compounds and agents are applied to the 10 growth or infection site in a formulation such as an ointment, cream, lotion, solution, tincture, or the like. Useful solid carriers include finely divided solids such as talc, clay, microcrystalline cellulose, silica, alumina and the like. Useful liquid carriers include water, alcohols or glycols or water-alcohol/glycol blends, in which the compounds can be dissolved or dispersed at effective 15 levels, optionally with the aid of non-toxic surfactants. Adjuvants such as fragrances and additional antimicrobial agents can be added to optimize the properties for a given use. The resultant liquid compositions can be applied from absorbent pads, used to impregnate bandages and other dressings, or sprayed onto the affected area using pump-type or aerosol sprayers, for example. 20 Thickeners such as synthetic polymers, fatty acids, fatty acid salts and esters, fatty alcohols, modified celluloses or modified mineral materials can also be employed with liquid carriers to form spreadable pastes, gels, ointments, soaps, and the like, for application directly to the skin of the user. Useful dosages of the compounds and agents and pharmaceutical compositions disclosed 25 herein can be determined by comparing their in vitro activity, and in vivo activity in animal models. Methods for the extrapolation of effective dosages in mice, and other animals, to humans are known to the art. Also disclosed are pharmaceutical compositions that comprise a compound disclosed herein in combination with a pharmaceutically acceptable carrier. Pharmaceutical compositions 30 adapted for oral, topical or parenteral administration, comprising an amount of a compound constitute a preferred aspect. The dose administered to a patient, particularly a human, should be sufficient to achieve a therapeutic response in the patient over a reasonable time frame, without lethal toxicity, and preferably causing no more than an acceptable level of side effects or morbidity. One skilled in the art will recognize that dosage will depend upon a variety of factors 35 including the condition (health) of the subject, the body weight of the subject, kind of concurrent 32 WO 2013/134467 PCT/US2013/029521 treatment, if any, frequency of treatment, therapeutic ratio, as well as the severity and stage of the pathological condition. Kits The disclosed subject matter also concerns a packaged dosage formulation comprising in 5 one or more containers at least one inhibitor compound or composition disclosed herein, e.g., any compound of Formulas I through II. A packaged dosage formulation can optionally comprise in one or more containers a pharmaceutically acceptable carrier or diluent. A packaged dosage formulation can also optionally comprise, in addition to an inhibitor compound or composition disclosed herein, other HDAC inhibitors, or an immunotherapeutic such as 10 ipilimumab. Depending upon the disorder or disease condition to be treated, a suitable dose(s) can be that amount that will reduce proliferation or growth of the target cell(s). In the context of cancer, a suitable dose(s) is that which will result in a concentration of the active agent in cancer tissue, such as a malignant tumor, which is known to achieve the desired response. The preferred 15 dosage is the amount which results in maximum inhibition of cancer cell growth, without unmanageable side effects. Administration of a compound and/or agent can be continuous or at distinct intervals, as can be determined by a person of ordinary skill in the art. To provide for the administration of such dosages for the desired therapeutic treatment, in some embodiments, pharmaceutical compositions disclosed herein can comprise between 20 about 0.l1% and 45 %, and especially, 1 and 150%, by weight of the total of one or more of the compounds based on the weight of the total composition including carrier or diluents. Illustratively, dosage levels of the administered active ingredients can be: intravenous, 0.01 to about 20 mg/kg; intraperitoneal, 0.01 to about 100 mg/kg; subcutaneous, 0.01 to about 100 mg/kg; intramuscular, 0.01 to about 100 mg/kg; orally 0.01 to about 200 mg/kg, and preferably 25 about I to 100 mg/kg; intranasal instillation, 0.01 to about 20 mg/kg; and aerosol, 0.01 to about 20 mg/kg of animal (body) weight. Also disclosed are kits that comprise a composition comprising a compound disclosed herein in one or more containers. The disclosed kits can optionally include pharmaceutically acceptable carriers and/or diluents. In one embodiment, a kit includes one or more other 30 components, adjuncts, or adjuvants as described herein. In another embodiment, a kit includes one or more anti-cancer agents, such as those agents described herein. In one embodiment, a kit includes instructions or packaging materials that describe how to administer a compound or composition of the kit. Containers of the kit can be of any suitable material, e.g., glass, plastic, metal, etc., and of any suitable size, shape, or configuration. In one embodiment, a compound 35 and/or agent disclosed herein is provided in the kit as a solid, such as a tablet, pill, or powder 33 WO 2013/134467 PCT/US2013/029521 form. In another embodiment, a compound and/or agent disclosed herein is provided in the kit as a liquid or solution. In one embodiment, the kit comprises an ampoule or syringe containing a compound and/or agent disclosed herein in liquid or solution form. EXAMPLES 5 The following examples are set forth below to illustrate the methods, compositions, and results according to the disclosed subject matter. These examples are not intended to be inclusive of all aspects of the subject matter disclosed herein, but rather to illustrate representative methods, compositions, and results. These examples are not intended to exclude equivalents and variations of the present invention, which are apparent to one skilled in the art. 10 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 is at or near atmospheric. There are numerous variations and combinations of reaction conditions, e.g., component concentrations, temperatures, pressures, and other reaction ranges 15 and conditions that can be used to optimize the product purity and yield obtained from the described process. Only reasonable and routine experimentation will be required to optimize such process conditions. 1 H and 13 C spectra were obtained on a Bruker spectrometer with TMS as an internal standard. The following abbreviations for multiplicity were used: s = singlet, d = doublet, t = 20 triplet, m = multiplet, dd = double doublet, br = broad. Reactions were monitored by TLC using precoated silica gel plates (Merck silica gel 60 F 25 4 , 250 gm thickness) and visualized under UV light. LRMS experiments were carried out using an Agilent 1946A LC-MSD with MeCN and
H
2 0 spiked with 0.10% formic acid as mobile phase. HRMS determinations were done with a Shimadzu IT-TOF instrument with MeCN and H 2 0 spiked with 0.l1% formic acid as mobile 25 phase. Flash chromatography was accomplished using the automated CombiFlash Rf system from Teledyne ISCO and prepacked silica gel cartridges according to the recommended loading capacity. Preparatory HPLC was used in purification of all final compounds using a Shimadzu preparative liquid chromatograph with the following specifications: Column: ACE 5AQ (150 x 30 21.2 mm) with 5 gm particle size. Method 1 - 25-100% MeOH/H 2 0, 30 min; 100% MeOH, 5 min; 100-25% MeOH/H 2 0, 4 min. Method 2 - 8-100% MeOH/H 2 0, 30 min; 100% MeOH, 5 min; 100-8% MeOH/H 2 0, 4 min. Method 3 - 0% MeOH, 5 min; 0-100% MeOH/H 2 0, 25 min; 100% MeOH, 5 min; 100-0% MeOH/H 2 0, 4 min. Flow rate = 17 mL/min with monitoring at 254 and 280 nm. Both solvents were spiked with 0.05% TFA. Analytical HPLC was carried out 35 using an Agilent 1100 series instrument with the following specifications: column: Luna 5 34 WO 2013/134467 PCT/US2013/029521 C18(2) 10OA (150 x 4.60 mm) 5 gm particle size; gradient - 10-100% MeOH/H 2 0, 18 min, 100% MeOH, 3 min; 100-10% MeOH/H 2 0, 3 min; 10% MeOH/H 2 0, 5 min. Both solvents were spiked with 0.05% TFA. The purity of all tested compounds was >95%, as determined by analytical HPLC. 5 Compound Synthesis: making reference to Scheme 1 Methyl 4-(((3-(dimethylamino)propyl)amino)methyl)benzoate (3a) The synthesis of 3a is representative, General Procedure A: A round-bottom flask charged with methyl 4-formyl benzoate (328 mg, 2 mmol) and 3-dimethylamino propylamine (0.252 mL, 2 mmol) was taken up in a solution of 5% AcOH in DCM (10 mL). After 5 minutes NaCNBH 3 (126 mg, 2 mmol) 10 was added in portions and the resulting mixture was allowed to stir at room temperature under an atmosphere of Ar overnight. The reaction was quenched with IN NaOH (10 mL) and the aqueous layer extracted with DCM (3x 1OmL). The combined organic extracts were washed with brine, dried over sodium sulfate, concentrated in vacuo and purified via flash chromatography affording the product as a waxy solid (313 mg, 63%). 'H NMR (400 MHz, 15 CDCl 3 ) 6 7.98 (d, J= 8.0 Hz, 2H), 7.38 (d, J= 8.0 Hz, 2H), 3.89 (s, 3H), 3.84 (s, 2H), 2.79 (br s, 1H), 2.68 (t, J= 6.8 Hz, 2H), 2.35 (t, J= 6.8 Hz, 2H), 2.23 (s, 6H), 1.70 (quint, J= 6.8 Hz, 2H). 1C NMR (100 MHz, CDCl3) 6 166.96, 145.27, 129.71, 128.87, 127.95, 58.04, 53.42, 51.99, 47.87, 45.36, 27.41. LRMS ESI: [M+H]* = 251.1 Methyl 4-(((3-hydroxypropyl)amino)methyl)benzoate (3b) Made according to General 20 Procedure A affording a waxy solid (89 mg, 29%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.00 (d, J= 8.0 Hz, 2H), 7.39 (d, J= 8.0 Hz, 2H), 3.91 (s, 3H), 3.90 (s, 2H), 3.78 (broad, 4H), 2.93 (t, J= 5.6 Hz, 2H), 1.78-1.73 (m, 2H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.79, 143.16, 129.77, 129.44, 128.26, 63.55, 53.14, 52.10, 48.88, 30.18. LRMS ESI: [M+H] = 224.2. Methyl 4-(((2-(1H-indol-3-yl)ethyl)amino)methyl)benzoate (3c) Made according to 25 General Procedure A affording a waxy solid (446 mg, 72%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.28 (br s, 1H), 7.98 (d, J= 8.0 Hz, 2H), 7.62 (d, J= 7.6 Hz, 1H), 7.36-7.34 (m, 3H), 7.21 (t, J= 7.6 Hz, 1H), 7.13 (t, J= 7.6 Hz, 1H), 7.00 (s, 1H), 3.92 (s, 3H), 3.87 (s, 2H), 3.02-2.98 (m, 4H), 1.68 (br s, 1H). 13 C NMR (100 MHz, CDCl 3 ) 6 167.06, 145.66, 136.34, 129.60, 128.62, 127.85, 127.31, 122.02, 121.89, 119.13, 118.74, 113.47, 111.15, 53.36, 51.97, 49.28, 25.64. LRMS ESI: 30 [M+H]Y = 309.1. Methyl 4-(((4-hydroxyphenethyl)amino)methyl)benzoate (3d) Made according to General Procedure A affording a waxy solid (130 mg, 46%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.97 (d, J= 8.0 Hz, 2H), 7.32 (d, J= 8.0 Hz, 2H), 7.01 (d, J= 8.4 Hz, 2H), 6.71 (d, J= 8.4 Hz, 2H), 3.90 (s, 3H), 3.86 (s, 2H), 2.86 (t, J= 6.8 Hz, 2H), 2.76 (t, J= 6.8 Hz, 2H). 1C NMR (100 MHz, 35 WO 2013/134467 PCT/US2013/029521 CDCl 3 ) 6 167.07, 154.60, 145.02, 131.05129.78, 129.75, 128.91, 128.04, 115.55, 53.29, 52.08, 50.37, 35.02. LRMS ESI: [M+H]* = 268.1. Methyl 4-(((3-methoxypropyl)amino)methyl)benzoate (3e) Made according to General Procedure A affording a colorless oil (127 mg, 54%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.94 (d, J= 5 8.0 Hz, 2H), 7.35 (d, J= 8.0 Hz, 2H), 3.86 (s, 3H), 3.80 (s, 2H), 3.41 (t, J= 6.4 Hz, 2H), 3.28 (s, 3H), 2.67 (t, J= 6.4 Hz, 2H), 1.72 (m, 2H). 1C NMR (100 MHz, CDCl 3 ) 6 166.88, 145.78, 129.54, 128.58, 127.76, 71.17, 58.48, 53.50, 51.85, 46.72, 29.83. LRMS ESI: [M+H]* = 238.2. Methyl 4-(((2-methoxyethyl)amino)methyl)benzoate (3f) Made according to General Procedure A affording a colorless oil (29 mg, 13%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.97 (d, J= 10 8.0 Hz, 2H), 7.38 (d, J= 8.0 Hz, 2H), 3.88 (s, 3H), 3.84 (s, 2H), 3.49 (t, J= 5.2 Hz, 2H), 3.33 (s, 3H), 2.77 (t, J= 5.2 Hz, 2H), 1.88 (br, 1H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.98, 145.58, 129.65, 128.74, 127.90, 71.85, 58.74, 53.47, 51.94, 48.69. LRMS ESI: [M+H] = 224.2. Methyl 4-((butylamino)methyl)benzoate (3g) Made according to General Procedure A affording colorless oil (150 mg, 68%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.99 (d, J= 8.0 Hz, 2H), 15 7.39 (d, J= 8.0 Hz, 2H), 3.91 (s, 3H), 3.84 (s, 2H), 2.62 (t, J= 7.2 Hz, 2H), 1.49 (m, 2H), 1.34 (m, 3H), 0.91 (t, J= 7.2 Hz, 3H). 1C NMR (100 MHz, CDCl 3 ) 6 167.00, 145.89, 129.65, 128.70, 127.87, 53.63, 51.95, 49.14, 32.14, 20.38, 13.93. LRMS ESI: [M+H] = 222.1. Methyl 4-((phenethylamino)methyl)benzoate (3h) Made according to General Procedure A affording a colorless oil (203 mg, 75%). 1H NMR (400 MHz, CDCl3) 6 8.01 (m, 20 2H), 7.35 (m, 4H), 7.22 (m, 3H), 3.93 (s, 3H), 3.88 (s, 2H), 2.89 (m, 4H). 13C NMR (100 MHz, CDCl3) 6 166.97, 145.66, 139.81, 129.65, 128.65, 128.43, 127.82, 126.15, 53.38, 51.96, 50.46, 36.29. LRMS ESI: [M+H]* = 270.1. Methyl 4-((1-(3-(dimethylamino)propyl)-3-(2-methoxyphenyl)ureido)methyl) benzoate (4a) The synthesis of 4a is representative, General Procedure B. A solution of 3a (99 25 mg, 0.395 mmol) in DCM (5 mL) was added the appropriate isocyante (0.053 mL, 0.395 mmol) at room temperature under and atmosphere of Ar and the resulting solution was allowed to stir overnight. The reaction was quenched with saturated bicarbonate (10 mL) and extracted with DCM (3x 10 mL). The combined organics were washed with brine (15 mL), dried over sodium sulfate, concentrated in vacuo and purified via flash chromatography affording the urea ester as a 30 waxy solid (156 mg, 98%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.64 (br s, 1H), 8.18 (d, J= 7.2 Hz, 1H), 7.99 (d, J= 8.0 Hz, 2H), 7.40 (d, J= 8.0 Hz, 2H), 6.97-6.94 (m, 2H), 6.84 (d, J= 7.2 Hz, 1H), 4.64 (s, 2H), 3.91 (s, 3H), 3.81 (s, 3H), 3.42 (t, J= 6.0 Hz, 2H), 2.34 (t, J= 6.0 Hz, 2H), 2.20 (s, 6H), 1.74 (quint, J= 6.0 Hz, 2H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.85, 156.64, 148.86, 143.75, 129.77, 129.43, 129.02, 127.53, 122.25, 120.94, 120.36, 109.92, 55.52, 54.60, 35 51.96, 49.19, 44.64, 44.18, 24.98. LRMS ESI: [M+H]* = 400.2. 36 WO 2013/134467 PCT/US2013/029521 Methyl 4-((1-(3-hydroxypropyl)-3-(2-methoxyphenyl)ureido)methyl)benzoate (4b) Made according to General Procedure B affording a waxy solid (113 mg, 74%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.07-8.03 (m, 3H), 7.39 (d, J= 8.0 Hz, 2H), 7.20 (br s, 1H), 6.93-6.90 (m, 2H), 6.77-6.47 (m, 1H), 4.59 (s, 2H), 3.91 (s, 3H), 3.67-3.62 (m, 7H), 1.80-1.77 (m, 2H). 1C NMR 5 (100 MHz, CDCl 3 ) 6 166.65, 156.31, 147.85, 142.24, 130.14, 129.70, 128.43, 126.77, 122.44, 121.04, 119.48, 109.88, 58.25, 55.53, 52.12, 50.41, 44.00, 30.32. LRMS ESI: [M+H] = 373.2. Methyl 4-((1-(2-(1H-indol-3-yl)ethyl)-3-(2-methoxyphenyl)ureido)methyl)-benzoate (4c) Made according to General Procedure B affording a solid (200 mg, 95%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.23-8.21 (m, 1H), 8.15 (br s, 1H), 7.99 (d, J= 8.0 Hz, 2H), 7.60 (d, J= 7.6 Hz, 10 1H), 7.36-7.34 (m, 3H), 7.22-7.10 (m, 3H), 7.02 (s, 1H), 6.97-6.94 (m, 2H), 6.81-6.79 (m, 1H), 4.59 (s, 2H), 3.91 (s, 3H), 3.70-3.67 (m, 5H), 3.12 (t, J= 7.6 Hz, 2H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.83, 155.17, 147.60, 143.28, 136.29, 129.98, 129.34, 128.79, 127.30, 127.13, 122.18, 122.08, 121.15, 119.51, 118.96, 118.46, 112.53, 111.29, 109.29, 55.56, 52.10, 50.89, 48.98. LRMS ESI: [M+H]* = 458.2. 15 Methyl 4-((1-(4-hydroxyphenethyl)-3-(2-methoxyphenyl)ureido)methyl)-benzoate (4d) Made according to General Procedure B affording a solid (178 mg, 90%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.15 (d, J= 4.8 Hz, 1H), 8.01 (d, J= 7.6 Hz, 2H), 7.35 (d, J= 8.0 Hz, 2H), 7.11 (s, 1H), 7.02 (d, J= 8.0 Hz, 2H), 6.95-6.93 (m, 2H), 6.80-6.77 (m, 3H), 6.43 (br s, 1H), 4.53 (s, 2H), 3.91 (s, 3H), 3.73 (s, 3H), 3.56 (t, J= 6.8 Hz, 2H), 2.87 (t, J= 6.8 Hz, 2H). 13 C NMR (100 20 MHz, CDCl 3 ) 6 166.89, 155.25, 154.99, 147.69, 142.93, 130.04, 129.83, 129.76, 129.40, 128.50, 127.21, 122.35, 121.18, 119.10, 115.67, 109.78, 55.60, 52.15, 50.97, 50.33, 33.88. LRMS: [M+H] = 435.2. Methyl 4-((1-(3-methoxypropyl)-3-phenylureido)methyl)benzoate (4e) Made according to General Procedure B affording a colorless oil (70 mg, 73%). 1 H NMR (400 MHz, 25 CDCl 3 ) 6 8.00 (d, J= 8.4 Hz, 2H), 7.84 (s, 1H), 7.45 (d, J= 8.4. Hz, 2H), 7.40 (d, J= 8.0 Hz, 2H), 7.30 (m, 2H), 7.02 (t, J= 7.6 Hz, 1H), 4.64 (s, 2H), 3.92 (s, 3H), 3.49 (t, J= 5.2 Hz, 2H), 3.44 (s, 3H), 3.415 (t, J= 6.4 Hz, 2H), 1.77 (m, 2H). 1C NMR (100 MHz, CDCl 3 ) 6 166.87, 156.36, 143.76, 139.85, 129.88, 129.18, 128.81, 127.72, 122.45, 119.17, 68.16, 58.63, 52.05, 49.41, 43.05, 27.55. LRMS ESI: [M+H]* = 358.2. 30 Methyl 4-((1-(2-methoxyethyl)-3-phenylureido)methyl)benzoate (4f) Made according to General Procedure B affording a colorless oil (40 mg, 910%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.33 (br, 1H), 8.02 (d, J= 8.0 Hz, 2H), 7.35 (m, 6H), 7.02 (t, J= 7.2 Hz, 1H), 4.68 (s, 2H), 3.93 (s, 3H), 3.50 (s, 3H), 3.46 (s, 4H). 1C NMR (100 MHz, CDCl 3 ) 6 166.88, 157.07, 143.81, 139.37, 129.92, 129.28, 128.81, 127.73, 122.34, 119.15, 72.59, 59.28, 52.07, 50.90, 48.44. 35 LRMS ESI: [M+H]* = 343.2. 37 WO 2013/134467 PCT/US2013/029521 Methyl 4-((1-butyl-3-phenylureido)methyl)benzoate (4g) Made according to General Procedure B affording colorless oil (59 mg, 98%). 'H NMR (400 MHz, CDCl 3 ) 68.04 (d, J= 8.0 Hz, 2H), 7.39 (d, J= 8.0 Hz, 2H), 7.27 (m, 4H), 7.03 (t, J= 7.2 Hz, 1H), 6.32 (s, 1H), 4.65 (s, 2H), 3.93 (s, 3H), 3.36 (t, J= 7.2 Hz, 2H), 1.64 (m, 2H), 1.37 (m, 2H), 0.96 (t, J= 7.2 Hz, 3H). 5 1C NMR (100 MHz, CDCl 3 ) 6 166.74, 155.30, 143.11, 138.83, 130.14, 129.50, 128.85, 127.04, 123.16, 119.90, 52.12, 50.49, 47.74, 30.52, 20.18, 13.81. LRMS ESI: [M+H]* = 341.1 Methyl 4-((1-phenethyl-3-phenylureido)methyl)benzoate (4h) Made according to General Procedure B affording a colorless oil (113 mg, 92%). 1 H NMR (400 MHz, CDCl 3 ) 6 8.02 (d, J= 8.4 Hz, 2H), 7.36 (m, 4H), 7.30 (d, J= 7.2 Hz, 1H), 7.21 (m, 4H), 7.08 (d, J= 8.0 10 Hz, 2H), 6.99 (t, J= 7.2 Hz, 1H), 6.00 (s, 1H), 4.58 (s, 2H), 3.91 (s, 3H), 3.59 (t, J= 6.8 Hz, 2H), 2.90 (t, J= 6.8 Hz, 2H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.71, 155.61, 142.99, 138.86, 138.72, 130.06, 129.43, 129.00, 128.86, 128.65, 127.28, 126.92, 122.95, 119.83, 52.08, 50.38, 49.94, 34.74. LRMS ESI: [M+H]* = 389.2. 4-((1-(3-(dimethylamino)propyl)-3-(2-methoxyphenyl)ureido)methyl)-N 15 hydroxybenzamide (5a) The synthesis of 5a is representative, General Procedure C. Solid NaOH (125 mg, 3.12 mmol) was dissolved in an aq. solution (5 0% wt, 1 mL) at 0 'C. Then a solution of 4a (156 mg, 0.390 mmol) in THF/MeOH (1:1, 6 mL total) was added dropwise where the biphasic solution became homogenous upon compete addition. The resulting solution was allowed to stir 30 min at room temperature. The reaction was quenched with AcOH (0.223 mL, 20 3.90 mmol) and concentrated in vacuo, and the crude product was purified via HPLC Method 2 and neutralized with bicarbonate wash affording the title compound (20 mg, 13%). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.22 (br s, 1H), 9.02 (br s, 1H), 7.80-7.76 (m, 3H), 7.39 (d, J= 8.4 Hz, 2H), 7.00-6.94 (m, 2H), 6.88-6.84 (m, 2H), 4.62 (s, 2H), 3.72 (s, 3H), 3.43-3.40 (m, 2H), 2.82 (br s, 2H), 2.56 (s, 6H), 1.91-1.86 (m, 2H). 1C NMR (100 MHz, DMSO-d 6 ) 6 155.35, 149.62, 25 141.56, 131.69, 128.60, 127.24, 127.15, 127.02, 123.14, 121.40, 120.23, 110.78, 55.62, 54.33, 49.32, 44.24, 42.76, 23.45. HRMS ESI: calc. for C 2 1
H
2 8
N
4 0 4 [M+H]* m/z = 401.2183; found 401.2164. N-hydroxy-4-((1-(3-hydroxypropyl)-3-(2-methoxyphenyl)ureido)methyl)-benzamide (5b) Made according to General Procedure C and purified via Method 3 affording the title 30 compound (95 mg, 84 %). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.19 (br s, 1H), 7.82 (d, J= 7.6 Hz, 1H), 7.76-7.71 (m, 3H), 7.37 (d, J= 8.0 Hz, 2H), 6.95 (d, J= 4.0 Hz, 2H), 6.88-06.85 (m, 1H), 4. 58 (s, 2H), 3.74 (s, 3H), 3.48 (t, J= 5.6 Hz, 2H), 3.40 (t, J= 6.8 Hz, 2H), 1.73-1.69 (m, 2H). 1 3 C NMR (100 MHz, DMSO-d 6 ) 6 164.10, 155.18, 149.08, 141.99, 131.56, 128.91, 127.18, 127.10, 126.93, 122.61, 120.49, 120.29, 110.76, 57.59, 55.69, 49.28, 43.97, 30.61. HRMS ESI: 35 calc. for C 19
H
2 3
N
3 0 5 [M+H]* m/z = 374.1710; found 374.1693. 38 WO 2013/134467 PCT/US2013/029521 4-((1-(2-(1H-indol-3-yl)ethyl)-3-(2-methoxyphenyl)ureido)methyl)-N hydroxybenzamide (5c) Made according to General Procedure C and purified via Method 1 affording the title compound (62 mg, 57%). 'H NMR (400 MHz, DMSO-d) 6 11.21 (br s, 1H), 10.86 (s, 1H), 10.12 (br s, 1H), 7.86 (t, J= 7.6 Hz, 1H), 7.75 (d, J= 8.0 Hz, 2H), 7.56 (d, J= 8.0 5 Hz, 1H), 7.42-7.40 (m, 3H), 7.34 (d, J= 8.0 Hz, 1H), 7.18 (s, 1H), 7.07 (t, J= 7.2 Hz, 1H), 7.01 6.96 (m, 3H), 6.90-6.86 (m, 1H), 4.64 (s, 2H), 3.71 (s, 3H), 3.62 (t, J= 7.6 Hz, 2H), 3.00 (t, J= 7.6 Hz, 2H). "C NMR (100 MHz, DMSO-d 6 ) 6 163.97, 158.37, 154.72, 148.88, 141.90, 136.21, 131.65, 128.70, 127.12, 122.98, 122.65, 120.97, 120.35, 118.31, 118.18, 111.41, 111.11, 110.66, 55.66, 49.77, 48.47, 23.89. HRMS ESI: calc. for C 2 6
H
2 6
N
4 0 4 [M+H]* m/z = 459.2027; found 10 459.2030. N-hydroxy-4-((1-(4-hydroxyphenethyl)-3-(2-methoxyphenyl)ureido)methyl) benzamide (5d) Made according to General Procedure C and purified via Method 2 affording the title compound (63 mg, 63%). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.20 (br s, 1H), 9.20 (br s, 1H), 7.82 (d, J= 8.0 Hz, 2H), 7.74 (d, J= 8.0 Hz, 2H), 7.38 (d, J= 8.4 Hz, 2H), 7.37 (s, 1H), 15 7.04 (d, J= 8.4 Hz, 2H), 6.98 (d, J= 8.0 Hz, 2H), 6.89-6.85 (m, 1H), 6.69 (d, J= 8.4 Hz, 2H), 4.57 (s, 2H), 3.75 (s, 3H), 3.49 (t, J= 7.6 Hz, 2H), 2.75 (t, J= 7.6 Hz, 2H). "C NMR (100 MHz, DMSO-d 6 ) 6 164.00, 155.76, 154.62, 148.97, 141.88, 131.63, 129.63, 128.83, 127.12, 122.72, 120.44, 120.33, 115.22, 110.69, 55.69, 49.68, 49.49, 33.21. HRMS ESI: calc. for C 2 4
H
2 5
N
3 0 5 [M+H]* m/z = 436.1867; found 436.1858. 20 N-hydroxy-4-((1-(3-methoxypropyl)-3-phenylureido)methyl)benzamide (5e) Made according to General Procedure C and purified via Method 2 affording the title compound (48 mg, 76%). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.19 (br, 1H), 8.36 (s, 1H), 7.72 (d, J= 8.4 Hz, 2H), 7.45 (d, J= 7.6 Hz, 2H), 7.32 (d, J= 8.4 Hz, 2H), 7.23 (m, 2H), 6.94 (t, J= 7.2 Hz, 1H), 4.61 (s, 2H), 3.34 (m, 4H), 3.21 (s, 3H), 1.74 (m, 2H). 1C NMR (100 MHz, DMSO-d 6 ) 6164.04, 25 155.30, 142.25, 140.42, 131.49, 128.31, 127.06, 121.87, 119.88, 69.16, 57.88, 49.08, 43.56, 27.81. HRMS ESI: calc. for C 19
H
2 3
N
3 0 4 [M+H]* m/z = 358.1761; found 358.1785. N-hydroxy-4-((1-(2-methoxyethyl)-3-phenylureido)methyl)benzamide (5f) Made according to General Procedure C and purified Method 2 affording the title compound (20 mg, 50%). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.17 (s, 1H), 9.01 (br, 1H), 8.44 (s, 1H), 7.72 (d, J= 30 8.0 Hz, 2H), 7.42 (d, J= 7.6 Hz, 2H), 7.32 (d, J= 8.0 Hz, 2H), 7.23 (t, J= 7.6 Hz, 2H)H, 6.94 (t, J= 7.2 Hz, 1H), 4.64 (s, 2H), 3.49 (s, 4H), 3.28 (s, 3H). 1C NMR (100 MHz, DMSO-d 6 ) 6 164.06, 155.46, 142.17, 140.30, 131.43, 128.32, 126.97, 121.83, 119.64, 70.88, 58.31, 49.82, 46.35. HRMS ESI: calc. for CisH 21
N
3 0 4 [M+H]* m/z = 344.1605; found 344.1601. 4-((1-butyl-3-phenylureido)methyl)-N-hydroxybenzamide (5g) Made according to 35 General Procedure C and purified by Method 2 affording the title compound (40 mg, 68%). 1 H 39 WO 2013/134467 PCT/US2013/029521 NMR (400 MHz, DMSO-d 6 ) 6 11.17 (br, 1H), 8.36 (s,1H), 7.72 (d, J= 8.0 Hz, 2H), 7.46 (d, J= 7.6 Hz, 2H), 7.32 (d, J= 8.0 Hz, 2H), 7.22 (t, J= 7.6 Hz, 2H), 6.94 (t, J= 7.2 Hz, 1H), 4.62 (s, 2H), 3.30 (m, 1H), 1.48 (m, 2H), 1.27 (m, 2H), 0.86 (t, J= 7.6 Hz, 3H). "C NMR (100 MHz, DMSO-d 6 ) 6 164.01, 155.22, 142.30, 140.45, 131.42, 128.19, 127.00, 126.96, 121.80, 120.04, 5 49.01, 46.11, 29.64, 19.43, 13.77. HRMS ESI: calc. for C 19
H
2 3
N
3 0 3 [M+H]* m/z = 342.1812; found 342.1802. N-hydroxy-4-((1-phenethyl-3-phenylureido)methyl)benzamide (5h) Made according to General Procedure C and purified by Method 2 affording the title compound (71 mg, 63%). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.15 (br, 1H), 7.72 (d, J= 8.0 Hz, 2H), 7.45 (d, J= 8.0 Hz, 10 2H), 7.31 (d, J= 8.0 Hz, 2H), 7.24 (m, 7H), 6.95 (t, J= 7.2 Hz, 1H), 4.60 (s, 2H), 3.54 (t, J= 7.6 Hz, 2H), 2.82 (t, J= 7.6 Hz, 2H). 1C NMR (100 MHz, DMSO-d 6 ) 6 164.04, 155.12, 142.12, 140.35, 139.04, 131.50, 128.77, 128.31, 128.20, 127.09, 127.05, 126.16, 121.91, 120.13, 49.20, 48.04, 33.91. HRMS ESI: calc. for C 2 3
H
2 3
N
3 0 3 [M+H]* m/z = 390.1812; found 390.1793. Compund Synthesis: makin reference to Scheme 2 15 N-butylaniline (6a) Was synthesized in an analogous manner previously reported (Org Lett, 4, 581). Briefly, Cul (19 mg, 0.1 mmol) and freshly ground K 3 P0 4 (849 mg, 4 mmol) were placed in a sealed tube followed by sequential addition of isopropanol (2 mL), ethylene glycol (0.222 mL, 4.0 mL), phenyl-iodide (0.224 mL, 2.0 mmol) and n-butylamine (0.237 mL, 2.4 mmol). The tube was then sealed and stirring commenced at 80 'C for 18 h. After cooling 20 to room temperature the reaction was diluted with water:ethyl ether (1:1, 10 mL). The aqueous layer was extracted with ether (3x 5mL), washed with brine (15 mL), dried over sodium sulfate and concentrated in vacuo. Purification via flash chromatography afforded the title compound as a yellow oil (235 mg, 79%). 1 H NMR (400 MHz, CDC 3 ) 6 7.19 (m, 2H), 6.70 (t, J= 7.2 Hz, 1H), 6.61 (d, J= 8.4 Hz, 2H), 3.60 (br, 1H), 3.12 (t, J= 7.2 Hz, 2H), 1.62 (m, 2H), 1.44 (m, 2H), 25 0.98 (t, J= 7.2 Hz, 3H). Spectra matches that reported in Okano et al., "Synthesis of secondary arylamines through copper-mediated intermolecular aryl amination," Org Lett 2003, 5(26):4987 4990. N-(3-methoxypropyl)aniline (6b) Made following the same procedure for 6a affording a light yellow oil (282 mg, 85%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.18 (m, 2H), 6.69 (t, J = 7.2 30 Hz, 1H), 6.61 (d, J= 8.4 Hz, 2H), 3.92 (br, 1H), 3.52 (t J= 6.0 Hz, 2H), 3.60 (s, 3H), 3.23 (t, J 6.8 Hz, 2H), 1.90 (m, 2H). Spectra matches that reported in Guo et al., Efficient Iron-Catalyzed N-Arylation of Aryl Halides with Amines," Org Lett 2008, 10(20):4513-4516. Methyl 4-((3-butyl-3-phenylureido)methyl)benzoate (7a) Methyl 4 (aminomethyl)benzoate hydrochloride (101 mg, 0.5 mmol) was taken up in a biphasic solution 35 of DCM:sat. bicarbonate (1:1, 4 mL) and added triphosgene (49 mg, 0.17 mmol) at 0 'C. After 40 WO 2013/134467 PCT/US2013/029521 30 min, the aqueous layer was extracted with DCM (3x 5mL), washed with brine (15 mL) and concentrated in vacuo. The crude isocyante was taken up in DCM (2 mL) and added 6a (75 mg, 0.5 mmol) and Et 3 N (0.209 mL, 1.5 mmol) and resulting solution allowed to stir overnight at room temperature. The reaction was quenched with with sat. bicarbonate (5 mL) and extracted 5 with DCM (3x 5mL). The combined organics were washed with brine (15 mL), dried over sodium sulfate, concentrated in vacuo. The crude material was purified via flash chromatography affording the title compound as an off-white waxy solid (93 mg, 55%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.95 (d, J= 8.0 Hz, 2H), 7.42 (t, J= 7.6 Hz, 2H), 7.32 (m, 1H), 7.25 (m, 4H), 4.45 (t, J= 5.6 Hz, 1H), 4.41 (d, J= 6.0 Hz, 2H), 3.89 (s, 3H), 3.70 (t, J= 7.6 Hz, 2H), 10 1.48 (m, 2H), 1.31 (m, 2H), 0.89 (t, 7.2 Hz, 3H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.89, 156.87, 145.14, 141.61, 130.08, 129.78, 128.85, 128.73, 127.81, 126.96, 52.01, 49.21, 44.25, 30.68, 19.92, 13.82. LRMS ESI: [M+H]* = 341.1. Methyl 4-((3-(3-methoxypropyl)-3-phenylureido)methyl)benzoate (7b) Made according to that of 7a except using 6b as the secondary amine affording the title compound as 15 an off-white waxy solid (65 mg, 3 6%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.96 (d, J= 8.0 Hz, 2H), 7.43 (t, J= 7.6 Hz, 2H), 7.33 (m, 1H), 7.27 (m, 4H), 4.69 (br, 1H), 4.42 (6.0 Hz, 2H), 3.90 (s, 3H), 3.80 (t, J= 7.2 Hz, 2H), 3.43 (t, J= 6.4 Hz, 2H), 3.27 (s, 3H), 1.83 (m, 2H). 13 C NMR (100 MHz, CDCl 3 ) 6 166.88, 156.95, 145.05, 141.63, 130.10, 129.80, 128.90, 127.79, 127.00, 70.23, 58.54, 52.03, 46.86, 44.29, 28.82. LRMS ESI: [M+H]* = 357.1. 20 Methyl 4-((3-ethyl-3-phenylureido)methyl)benzoate (7c) Made according to that of 7a except using commercially available N-ethylaniline as the secondary amine affording the title compound as an off-white waxy solid (197 mg, 63%). 1 H NMR (400 MHz, CDCl 3 ) 6 7.94 (d, J= 8.4 Hz, 2H), 7.24 (t, J= 7.6 Hz, 2H), 7.32 (t, J= 7.2 Hz, 1H), 7.26 (m, 4H), 4.57 (br, 1H), 4.41 (d, J= 5.6 Hz, 1H), 3.88 (s, 3H), 3.76 (dd, J= 14, 7.2 Hz, 2H), 1.12 (t, J= 7.2 Hz, 3H). 13 C 25 NMR (100 MHz, CDCl 3 ) 6 166.82, 156.64, 145.09, 141.22, 130.03, 129.72, 128.79, 127.82, 126.92, 51.95, 44.17, 44.09, 13.82. LRMS ESI: [M+H]* = 313.1. 4-((3-butyl-3-phenylureido)methyl)-N-hydroxybenzamide (8a) Made according to General Procedure C and purified by Method 2 affording the title compound as an off-white solid (74 mg, 80%). 1 H NMR (400 MHz, DMSO-d 6 ) 6 11.13 (br, 1H), 8.72 (br, 1H), 7.66 (d, J 30 =8.0 Hz, 2H), 7.43 (t, J= 7.6 Hz, 2H), 7.27 (m, 5H), 6.23 (t, J= 5.6 Hz, 1H), 4.20 (d, J= 5.6 Hz, 2H), 3.57 (t, J= 6.8 Hz, 2H), 1.35 (m, 2H), 1.23 (m, 2H), 0.82 (t, J= 6.8 Hz, 3H). 1C NMR (100 MHz, DMSO-d 6 ) 6 164.17, 156.48, 144.50, 142.12, 130.129.55, 128.22, 126.67, 126.61, 48.44, 43.38, 30.21, 19.35, 13.72. HRMS ESI: calc. for C 19
H
2 3
N
3 0 3 [M+H]* m/z = 342.1812; found 342.1825. 41 WO 2013/134467 PCT/US2013/029521 N-hydroxy-4-((3-(3-methoxypropyl)-3-phenylureido)methyl)benzamide (8b) Made according to General Procedure C and purified by Method 2 affording an off-white solid (59 mg, 91%). 'H NMR (400 MHz, DMSO-d 6 ) 6 11.14 (br, 1H), 7.66 (d, J= 8.0 Hz, 2H), 7.43 (t, J= 7.6 Hz, 2H), 7.27 (m, 5H), 6.27 (t, J= 6.0 Hz, 1H), 4.21 (d, J= 5.8 Hz, 2H), 3.62 (t, J= 7.2 Hz, 2H), 5 3.28 (t, J= 6.4 Hz, 2H), 3.14 (s, 3H), 1.63 (m, 2H). "C NMR (100 MHz, DMSO-d 6 ) 6 164.13, 156.51, 144.44, 142.19, 130.89, 129.57, 128.18, 126.70, 126.64, 69.49, 57.80, 46.35, 43.39, 28.32. HRMS ESI: calc. for C 19
H
2 3
N
3 0 4 [M+H]* m/z = 358.1761; found 358.1749. 4-((3-ethyl-3-phenylureido)methyl)-N-hydroxybenzamide (8c) Made according to General Procedure C and purified by Method 2 affording an off-white solid (91 mg, 96%). 1 H 10 NMR (400 MHz, DMSO-d 6 ) 6 11.13 (br, 1H), 7.67 (d, J= 8.0 Hz, 2H), 7.43 (t, J= 7.6 Hz, 2H), 7.26 (m, 5H), 6.30 (t, J= 6.0 Hz, 1H), 4.21 (d, J= 5.6 Hz, 2H), 3.61 (dd, J= 14, 7.2 Hz, 2H), 0.99 (t, J= 7.2 Hz, 3H). 1C NMR (100 MHz, DMSO-d 6 ) 6 164.21, 156.34, 144.54, 142.00, 130.92, 129.57, 128.32, 126.75, 126.67, 43.70, 43.39, 13.76. HRMS ESI: calc. for C 17
H
19
N
3 0 3 [M+H]* m/z = 314.1499; found 314.1489. 15 HDAC inhibition assays HDAC inhibition assays were performed by Reaction Biology Corp. (Malvern, PA) using isolated human, recombinant full-length HDAC 1 and -6 from a baculovirus expression system in Sf9 cells. An acetylated fluorogenic peptide, RHKKAc, derived from residues 379-382 of p53 was used as substrate. The reaction buffer was made up of 50 mM Tris-HCl pH 8.0, 127 mM 20 NaCl, 2.7 mM KCl, 1 mM MgCl 2 , 1 mg/mL BSA, and a final concentration of 1% DMSO. Compounds were delivered in DMSO and delivered to enzyme mixture with preincubation of 5 10 min followed by substrate addition and incubation for 2 h at 30 'C. Trichostatin A and developer were added to quench the reaction and generate fluorescence, respectively. Dose response curves were generated starting at 30 gM compound with three-fold serial dilutions to 25 generate a 10-dose plot. IC 50 values were then generated from the resulting plots, and the values expressed are the average of duplicate trials ± standard deviation. Compound 1 was identified to possess submicromolar HDAC inhibitory activity; however, it was not selective against representative members of the Zn 2 -dependant Classes 1 and 2 (HDAC 1 and HDAC6, respectively). It was discovered that activity and selectivity could 30 be improved for HDAC6 by accessing a unique cavity on the surface of HDAC6. This was accomplished substitutions on the urea nitrogens. There is a shorter substrate channel on HDAC6 relative to HDAC 1 and this feature represented an excellent strategy to impart critical isoform selectivity (Butler et al., JAm Chem Soc 2010, 132(31):10842-10846; Kalin et al., J Med Chem 2012, 55(2):639-65 1). By incorporating substitutions on the urea motif, the 35 additional branched molecular surface could form valuable contacts with the subtle differences at 42 WO 2013/134467 PCT/US2013/029521 the HDAC6 surface while the benzyl linker would give a shorter linker that would favor away from HDACl inhibition. A summary of the HDACl and HDAC6 inhibitory data obtained is presented in Table 1. Table 1. HDAC inhibition screen of substituted urea compounds Compound Structure HDAC1 IC,, HDAC6 IC,, Fold Selective (nM) (nM) (HDAC1/HDAC6) 1 0 265 59 139 27 2 0 N'OH H H H N 'rN - 0 5a | 2550 540 458 64 6 N O N N OH H H SN YN - 0 5b HO 1910 570 2.38 0.38 803 OH N YNH - 0 5c HN 8950 770 468 130 19 0 N NNOH OH 0 N NO ~- 0 5d OH 1690 120 5.80 0.50 292 0 N N OH 5f 250 420 9.6 0.66 243 OH SN YN 0- 0 5f 0 0250+1320 1.7+10.76 443 00 43 WO 2013/134467 PCT/US2013/029521 5g o 3020 740 5.02 0.060 600 N NNOH 5h 3120 640 14.0 0.75 222 N OH H I H N N 8a 0 8120 600 25.2 2.5 322 N N O H 0 8b 1360 ±450 60.3 15.8 226 u 0 N OH HI H N Y~ 8c 0 1360 650 41.1 0.40 330 N ' NOH H H -- 0 9a 0 1060 8.3 128 N OH Hu H H
H
3 CO 9b 0 579 2.2 263 N'OH H H H N N N 9c 0 1000 6.9 145 NOH H H H N N NH 0 44 WO 2013/134467 PCT/US2013/029521 Tubastatin Ab 16400 260 15.0 0.01 1903 NHOH N TSAbc 5 1.0 1.2 0.30 4 N NHOH H3 MGCDO103 102 38 >10,000aIC 5 o displayed are the mean of two experiments standard deviation obtained from curve fitting of 10-point enzyme assay starting from 30 gM analog with 3-fold serial dilution. Values are extracted from fitting dose-response curves to the data points, b Butler et al., JAm Chem Soc c d 2010, 132(31):10842-10846; ' Trichostatin A; Fournel et al., "MGCDO103, a novel isotype 5 selective histone deacetylase inhibitor, has broad spectrum antitumor activity in vitro and in vivo," Mol Cancer Ther 2008, 7(4):759-768. The analogs based on 1 maintained the same 2-methoxyphenyl cap group but contained varied substitutions on the proximal linking nitrogen of the urea (5a-d). Introducing the 10 branching element at this position had a dramatic impact on decreasing activity at HDAC 1. Interestingly, inhibition at HDAC6 was found to be dependent upon the nature of this substitution. The dimethylamino substitution as in 5a, and the 3-indoyl substitution as in 5c, both proved detrimental to HDAC6 inhibition as they were over three times less potent compared to compound 1. They did however, maintain low micromolar inhibitory activity at 15 HDAC1; but the activity against HDAC6 was only in the submicromolar range. As the tertiary amine in 5a would be protonated at physiological pH, it is possible that a positive charge is unfavorable for proper target binding. Likewise, the larger indole group of 5c may simply present too much steric bulk to be properly accommodated by the active site. However, the 3 hydroxypropyl derivative, 5b, and the 4-hydroxyphenylethyl derivative, 5d, resulted in a 20 significant increase in the inhibition of HDAC6. These substitutions had only a marginal effect on HDAC 1 activity. It is possible the hydroxyl groups of 5b and 5d are able to serve as H-bond acceptors or donors and possess favorable interactions with key amino acid residues on the HDAC6 surface, thus improving binding affinity. 45 WO 2013/134467 PCT/US2013/029521 The first series of compounds based on 1 maintained the 2-methoxy group in the aryl urea cap. The oxidative potential of phenols presents a substantial hurdle for in vivo efficacy thus the structure activity relationship (SAR) investigation was furthered by synthesizing a series with a phenyl cap using the same chemistry. To demonstrate the influence of an H-bond 5 acceptor the the free hydroxyl moeity was masked. Capping the free hydroxyl with a methyl group resulted in 5e, and was also found to be a low nanomolar inhibitor with >400 fold selectivity for HDAC6. Shortening to an ethylene bridge in 5f did not significantly dissuade HDAC6 inhibition, but did slightly increase activity against HDAC 1 ultimately lowering the selectivity for HDAC6. The general trend established was that an H-bond donor and large 10 aromatic groups deterred activity, whereas smaller groups with H-bond acceptors were favored for selective HDAC6 activity. Interestingly, the n-butyl 5g and phenethyl 5h were proficient HDAC6i in the low nanomolar range with 5g possessing excellent selectivity over HDAC 1 (600 fold). These data refute the notion that a specific H-bond interaction is required for activity. Shifting the branching element to the distal urea nitrogen resulted in analogs 8a-c. The 15 most potent of this series, 8a, possessed the same n-butyl substitution as 5e. While 8a is a nanomolar HDAC6I, it is five-times less potent and more importantly, is less selective than the proximally substituted homolog 5e. The methoxy variant 8b suffered a dramatic decrease in potency towards HDAC6. Whereas the alkyl to heteroalkyl switch on the proximal nitrogen resulted in equipotent inhibition on the distal nitrogen, this modification was detrimental to 20 furthering potent HDAC6I development. Decreasing the length of the alkyl branch in 8c also resulted in decreased HDAC6 inhibition. These data point to specific requirements for inhibitors decorated with a cap groups comprising of an acyclic urea and that potent and selective inhibition comes most from urea substitutions on the proximal nitrogen to generate a branched cap group. 25 Evaluating the disclosed compounds against other HDACi's developed by others reveals 5g, termed "Nexturastat A," is in fact a potent and selective HDAC6i. Comparing for example, 5g to Tubastatin A, another HDAC6i (Butler et al., JAm Chem Soc 2010, 132(31):10842 10846), reveals that the inhibition of HDAC6 has been improved while maintaining excellent selectivity relative to HDAC 1. 5g also demonstrates comparable HDAC6 potency to 30 Trichostatin A (TSA) (see Table 1). Additionally, the amino-benzamide ZBG has been incorporated into the HDACi's, and its introduction reduces Class 2 inhibition resulting in Class 1 selectivity; this is typified by MGCDO 103, an HDACI that possesses antiproliferative activity and that has recently entered clinical trials (Zhou et al., "Discovery of N-(2-aminophenyl)4- 4 pyridin-3-ylpyrimidin-2-ylamino)methyl benzamide (MGCDO103), an orally active histone 46 WO 2013/134467 PCT/US2013/029521 deacetylase inhibitor," JMed Chem 2008, 51(14):4072-4075). Compared to MGCDO103, 5g leads to a 30-fold reduction in activity at HDAC1. Similar experiments were done with compounds 1Oa, 1Ob, and 11a , which are cyclic ureas of Formula I-C (Table 2). 5 Table 2. HDAC scree of cyclic urea compounds Compound HDACl IC 50 HDAC6 1C 5 0 Fold Selective (nM) (nM) (HDAC1/HDAC6) 10a 28600 74.2 386 10b 11800 22.2 531 11a 7560 25.6 295 Since the HDAC isoforms are highly homologous obtaining selectivity is critical for avoiding off-target effects and is paramount for the development of the disclosed HDAC6i's. It is well known that Class 1 inhibition is responsible for the cytotoxicity associated with pan 10 selective HDACi; thus, 5g was screened against all 11 isoforms (Table 3). In the similar Class 1 and Class 4 isoforms, 5g displayed low micromolar activity compared to the low nanomolar activity of HDAC6. Moreover, 5g demonstrated high levels of selective inhibition against members of the related Class 2 HDAC isforms reaching >1000-fold selective in some cases. These data establish 5g, and similar analogs, to be potent and isoform selective HDAC6i's. 15 Table 3. Inhibitory profile of 5g against HDAC1-11a Isoform IC 50 Fold selective for (gM) HDAC6 HDAC1 3.02 1.04 600 HDAC2 6.92 0.763 1380 HDAC3 6.68 1.75 1330 HDAC4 9.39 0.863 1870 HDAC5 11.7 0.141 2330 HDAC6 0.00502 0.00060 - HDAC7 4.46 0.665 888 HDAC8 0.954 0.0799 190 HDAC9 6.72 1.15 1340 HDAC10 7.57 0.481 1510 HDAC11 5.14 0.686 1020 47 WO 2013/134467 PCT/US2013/029521 aIC 5 o displayed are the mean of two experiments ± standard deviation obtained from curve fitting of 10-point enzyme assay starting from 30 gM analog with 3-fold serial dilution. Values are extracted from fitting dose-response curves to the data points. 5 Tubulin and histone acetylation western blot assay The ability of 5g to induce hyperacetylation of a-tubulin, a hallmark of HDAC6 inhibition, without elevating levels of acetylated histones was evaluated. B 16 melanoma cells were plated at 10 5 cells/well in 12 well plates and allowed to adhere overnight. A 50 mM stock of compound was then added by serial dilutions in complete medium to the indicated 10 concentrations. Cells were incubated for 24 h under humidified conditions (37 0 C, 5% CO 2 ). Wells were then washed with cold PBS, and cells were lysed in a buffer containing 10 mM Tris HCl pH 8.0, 10% SDS, 4 mM urea, 100 mM DTT, and 1x protease inhibitor (Roche). Cells were lysed for 30 min on ice and then sonicated for 8 min (8 cycles of 30 s on/ 30 s rest). Cells were then boiled for 10 min with 6x gel loading buffer and resolved on 4-15 % gradient gels and 15 subsequently transferred onto nitrocellulose membranes. Membranes were blocked with 5% milk in PBS-T and detection of specific antigens using antibodies against acetyl-H3 and H3 (Cell Signaling), and acetyl- a-tubulin and a-tubulin (Sigma). Bands were detected by scanning blots with LI-COR Odyssey imaging system using both 700 and 800 channels. HDAC6 contains two catalytic domains. Its C-terminus domain is the functional domain 20 for both synthetic and physiological substrates, whereas the N-terminal domain is devoid of enzymatic activity (Zou et al., "Characterization of the two catalytic domains in histone deacetylase 6," Biochem Biophys Res Commun 2006, 341(1):45-50). Low nanomolar treatement of 5g on B 16 murinemelanoma cells led to a dose-dependant increase of acetyl a-tubulin levels without a concamanent elevation of histone H3 acetylation (Figure 39) indicating binding to the 25 second, enzymatically-active catalytic domain. Not until concentrations of 1 and 10 [tM were used was an observable increase in histone H3 acetylation found. This was expected as the biochemical IC 50 of 5g against the Class 1 HDACs, those responsible for histone acetylation, is in the micromolar range. There is a clear preference for activity of 5g in a cellular environment that corresponds to selective HDAC6 inhibition. 30 B16 melanoma cell growth inhibition assay Compounds were evaluated in an MTS assay to determine the ability of selective HDAC6i to exert an antiproliferative effect on B16 murine melanoma cells. B16 murine melanoma cells were plated at 5x10 3 /well in 96 well flat bottom plates. The following day, media was changed to that containing various concentrations of HDACi or matched DMSO 35 vehicle concentrations diluted in complete medium done in triplicate. Cells were incubated for 48 WO 2013/134467 PCT/US2013/029521 48 hours at 37 0 C and 5% CO 2 . Density of viable, metabolically active cells was quantified using a standard MITS assay (CellTiter 96 AQueous One, Promega, Madison, WI) as per manufacturer's instructions. Briefly, 20tL of reagent were added per well and incubated at 37 0 C for 3 hours. Absorbances at 490 nM were measured spectrophotometrically with background 5 subtraction at 690nM. All values were then normalized and expressed as a percentage of medium control (100%). Treatment with the compounds for 48 h resulted in dose-dependent growth inhibition of the oncogenic melanoma cells summarized in Table 4. The general trend for inhibiting cell growth correlates with potency for HDAC6. However, the potent and selective 5b, performed 10 very poorly in the cellular assay possibly due to it being highly polar and lacking efficient cell permeability. Comparing the most active compounds 5d and 5f-h in this whole-cells assay reveals that the most selective HDAC6i's have the greatest efficacy in inhibiting cell growth. It should also be noted that they also have higher cLogP values, possibly contributing to improved cell permeability. As the cLogP is adjusted to more optimal levels, as exemplified for 5g (cLogP 15 = 2.20), cellular efficacy is restored, demonstrating that a proper balance of physiochemical parameters must be maintained. Table 4. Antiproliferative activity against B16 murine melanoma cells Compound G1 50 (pM) 5a 75.3 1.23 5b >100 5c 30.4 ± 1.32 5d 18.4 1.23 5e 22.2 1.41 5f 19.1 + 1.19 5g 14.3 1.15 5h 15.4 1.20 8a 65.8 1.19 8b >100 8c >100 Tubastatin 40.5 + 1.21 LBH589 0.150 49 WO 2013/134467 PCT/US2013/029521 Compared to the pan-selective HDACi LBH589, 5g is approximately 100-fold less potent in inducing murine B 16 melanoma cell death. This decreased efficacy is unlikely due to poor cell permeability, for as shown above, the treatment of B 16 cells with nanomolar doses of 5g results in increased acetyl-tubulin levels (Figure 39). Additionally, both compounds possess 5 similar cLogP values (2.64 vs 2.20 for LBH589 and 5g, respectively). Rather, the effects of nonselective HDAC inhibition with LBH589 treatment are likely contributing to its increased potency, and in particular, its Class 1 activity. It is also of interest to note that 5g has increased potency against the B 16 cell line in comparison to Tubastatin A (Table 4). While a definitive explanation for this difference in cellular activity is lacking, it is possible that this is due to the 10 improved HDAC6 activity of 5g. While HDAC6-selective inhibitors have not played a role in cancer therapy to date, the data indicate that they have utility in this area. This work thus constitutes the first report of HDAC6 selective inhibitors that possess antiproliferative effects against melanoma cells. The materials and methods of the appended claims are not limited in scope by the 15 specific materials and methods described herein, which are intended as illustrations of a few aspects of the claims and any materials and methods that are functionally equivalent are within the scope of this disclosure. Various modifications of the materials and methods in addition to those shown and described herein are intended to fall within the scope of the appended claims. Further, while only certain representative materials, methods, and aspects of these materials and 20 methods are specifically described, other materials and methods and combinations of various features of the materials and methods are intended to fall within the scope of the appended claims, even if not specifically recited. Thus a combination of steps, elements, components, or constituents can be explicitly mentioned herein; however, all other combinations of steps, elements, components, and constituents are included, even though not explicitly stated. 25 50

Claims (29)

1. A compound having Formula I: A N 0 wherein A is aryl, heteroaryl, or C 1 -Cs alkyl, any of which is optionally substituted with one or more groups chosen from acetyl, CI-C 5 alkyl, amino, -NR 6 R 7 , C(O)NR 6 R 7 , C 1 -C 4 alkoxy, C 1 -C 4 alkylhydroxy, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, heteroaryl, halo, hydroxy, thiol, cyano, or nitro; and R and R 2 are independently chosen from hydrogen, C 1 -Cs alkyl, CI-Cs alkenyl, C1 Cs alkynyl, C 1 -Cs haloalkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, CI-C 3 alkylaryl, aryl, C 1 -C 3 alkylheteroaryl, or heteroaryl, any of which is optionally substituted with acetyl, C 1 -C 5 alkyl, amino, -NR 6 R 7 , -C(O)NR 6 R 7 , C 1 -C 4 alkoxy, C 1 -C 4 alkylhydroxy, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, heteroaryl, carbonyl, halo, hydroxy, thiol, cyano, or nitro; or R and R 2 are joined such that together they form an alkylene bridge comprising 2 atoms so that a 5-membered ring is formed with the -NC(O)N- moiety, in which case A is as defined above or hydrogen, and which 5-membered ring is optionally substituted with R', R 2 ', R 1 ", and R2", which are independently, hydrogen, or are C 1 -Cs alkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, C 1 -C 3 alkylaryl, aryl, C 1 -C 3 alkylheteroaryl, or heteroaryl any of which is optionally substituted with amino, aryl, C 1 -C 4 alkoxy, halo, or hydroxy; or R' and R 1 " together or R2" and R2' together form a carbonyl (i.e., =0); or R' and R 2 ' are null and R 1 " and R 2 " together form a fused phenyl group; and 51 WO 2013/134467 PCT/US2013/029521 R6 and R 7 are independently H, C 1 -C 4 alkyl, or are joined such that together they form an alkylene bridge comprising 4 or 5 atoms so that a 5 or 6-membered ring is formed with the nitrogen; or a pharmaceutically acceptable salt or hydrate thereof.
2. The compound of claim 1, wherein R 1 and R 2 are both hydrogen, A is not hydroxyphenyl.
3. The compound of any of the previous claims, wherein A is phenyl, pyridyl, oxazolidyl, or pyrimidyl optionally substituted with C 1 -C 5 alkyl, amino, alkoxy, alkylhydroxy, halo, hydroxy, or thiol.
4. The compound of any of the previous claims, wherein A is phenyl.
5. The compound of any of the previous claims, wherein A is phenyl substituted with one or more C 1 -C 5 alkyl, C 1 -C 4 alkoxyl, or halo.
6. The compound of any of the previous claims, wherein A is ortho-methoxyl substituted phenyl.
7. The compound of any of the previous claims, wherein A is pyridyl or pyridyl substituted with C 1 -C 5 alkyl, C 1 -C 4 alkoxyl, or halo.
8. The compound of any of the previous claims, wherein A is n-propyl, i-propyl, n butyl, t-butyl, s-butyl, i-butyl, n-pentyl, i-pentyl, or s-pentyl group.
9. The compound of any of the previous claims, wherein R 1 is hydrogen, CI-Cs alkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with C 1 -C 3 alkyl, amino, -NR 6 R 7 , C 1 -C 4 alkoxy, C 1 -C 4 alkylhydroxy, carbonyl, hydroxy, thiol, or cyano.
10. The compound of any of the previous claims, wherein R 1 is C 1 -CS alkyl.
11. The compound of any of the previous claims, wherein R 1 is CI-CS alkyl which is optionally substituted with acetyl, NH 2 , N(C 1 -C 4 ) 2 C 1 -C 4 alkoxy, C 1 -C 4 C 5 -C 6 heterocycloalkyl, carbonyl, halo, or hydroxy.
12. The compound of any of the previous claims, wherein R 1 is hydrogen. 52 WO 2013/134467 PCT/US2013/029521
13. The compound of any of the previous claims, wherein R 2 is hydrogen, CI-Cs alkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with CI-C 5 alkyl, amino, -NR 6 R 7 , C 1 -C 4 alkoxy, C 1 -C 4 alkylhydroxy, carbonyl, hydroxy, thiol, or cyano.
14. The compound of any of the previous claims, wherein R2 is C 1 -C 5 alkyl, or C1-Cs alkyl substituted with a methoxy, amino, -NR 6 R 7 , alkylhydroxy, carbonyl, hydroxy, cyano.
15. The compound of any of the previous claims, wherein R2 is C 1 -C 4 alkyl substituted with a heteroaryl.
16. The compound of any of the previous claims, wherein R2 is CI-C 4 alkyl substituted with a phenyl, hydroxy substituted phenyl, methoxy substited phenyl, halo substituted phenyl, or amino substituted phenyl.
17. The compound of any of the previous claims, wherein the compound has Formula I A: R2 NHOH H W N N "W 0 R5 I-A wherein each W is independent of the others CH or N; and R 5 is hydrogen, C 1 -Cs alkyl, C 1 -Cs alkenyl, C 1 -Cs alkynyl, C 1 -Cs haloalkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with acetyl, C 1 -C 5 alkyl, amino, -NR 6 R 7 , -C(O)NR 6 R 7 , CI-C 4 alkoxy, CI-C 4 alkylhydroxy, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, heteroaryl, carbonyl, halo, hydroxy, thiol, cyano, or nitro, or a pharmaceutically acceptable salt or hydrate thereof.
18. The compound of any of the previous claims, wherein the compound has Formula I B: 53 WO 2013/134467 PCT/US2013/029521 00 R' NHOH IH w N N R 5 I-B wherein each W is independent of the others CH or N; and R 5 is hydrogen, C 1 -Cs alkyl, C 1 -Cs alkenyl, C 1 -Cs alkynyl, C 1 -Cs haloalkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, or heteroaryl, any of which is optionally substituted with acetyl, C 1 -C 5 alkyl, amino, -NR 6 R 7 , -C(O)NR 6 R 7 , CI-C 4 alkoxy, CI-C 4 alkylhydroxy, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, heteroaryl, carbonyl, halo, hydroxy, thiol, cyano, or nitro, or a pharmaceutically acceptable salt or hydrate thereof.
19. The compound of any of the previous claims, wherein the compound has Formula I C: R 1"U R 2-,R 2 R1 NHOH A N N 0 I-C wherein A is hydrogen, or A is aryl, heteroaryl, or C 1 -Cs alkyl, any of which is optionally substituted with one or more groups chosen from acetyl, C 1 -C 5 alkyl, amino, -NR 6 R 7 , -C(O)NR 6 R 7 , C 1 -C 4 alkoxy, C 1 -C 4 alkylhydroxy, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, aryl, heteroaryl, halo, hydroxy, thiol, cyano, or nitro, with R 6 and R 7 as defined above; and RI , R2 , R ", and R 2 ", are independently, hydrogen, or are C 1 -CS alkyl, C 5 -C 6 cycloalkyl, C 5 -C 6 heterocycloalkyl, C 1 -C 3 alkylaryl, aryl, C 1 -C 3 alkylheteroaryl, or heteroaryl any of which is optionally substituted with amino, aryl, C 1 -C 4 alkoxy, halo, or hydroxy; or R' and R 1 " together or R2" and R 2 ' together form a carbonyl; or R' and R 2 ' are null and R 1 " and R 2 " 54 WO 2013/134467 PCT/US2013/029521 together form a fused phenyl group, or a pharmaceutically acceptable salt or hydrate therof.
20. The compound of any of the previous claims, wherein R' and R 1 " or R 2 ' and R 2 " are both methyl.
21. The compound of any of the previous claims, wherein R' is hydrogen and R 1 " is methyl, ethyl, propyl, i-propyl, n-butyl, i-butyl, benzyl, tosyl, hydroxyphenyl, C 1 -C 4 alkoxyphenyl, or aminophenyl or R 2 ' is hydrogen and R 2 " is methyl, ethyl, propyl, i propyl, n-butyl, i-butyl, benzyl, tosyl, hydroxyphenyl, C 1 -C 4 alkoxyphenyl, or aminophenyl.
22. The compound of any of the previous claims, wherein R' and R 1 " or R 2 ' and R 2 , form a carboxyl group.
23. The compound of any of the previous claims, wherein the compound is chosen from: 0 1 0OH N OH5 N N 0N H H H -t 0 1 (t 0 5a HO 0 HN O N'OH 0 ~ N~ I0 NH d r 5b N N H I 0 5c OH U 0 S0OH N O N lN 5e 50 5d 55 WO 2013/134467 PCT/US2013/029521 00 0 N' OH N OH H NK-H S 0 0~ 5f 5g 0 N.0 k N OH ~yN~ K H N) 8a 00 00 u0 N' NOH ,O H IH HI HNyN y 0 8c 0 8b 0 0 k. N OH N' NOH H. K- H H 3 00 0 0~~I 9a 9b o 0 N' H N NOH H H H N N N N 0 9c Br ,a 0 o 0 N. OH O H N. N N ~ - 0 - 0 F o o N. ,OH N. NOH H HIH N N NN N N 00 56 WO 2013/134467 PCT/US2013/029521 0 0 N NOH 'N N OH H H H N N N I N N N 0 0 00 0 0 0 S NOH OH rN H N N H 0 10a 0 10b O OH 0 H HN-H O aA N 'I H HN I H \N 0 Ila HO HO 0\ 0 00 -N OH 0 OH -NN O O' 0 0
24. A method of treating melanoma or mantle cell lymphoma in a subject, comprising: administering to the subject a therapeutically effective amount of a histone deacetylase inhibitor.
25. The method of claim 24, wherein the inhibitor is a histone deacetylase 6 inhibitor.
26. The method of any of claims 24-25, wherein the inhibitor is Tubstatin A.
27. The method of any of claims 24-26, wherein the inhibitor is a compound of any of claims 1-23.
28. The method of any of claims 24-27, wherein the inhibitor is administered with one or more of ipilimumab, revlimid, velcade, vemurafenib, ST-3-06, ST-2-92, Tubstatin A, Tubacin.
29. The method of any of claims 24-28, wherein the inhibitor is combined with a STAT3 inhibitor. 57
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