DETAILED DESCRIPTION OF THE INVENTION

[0052] The present invention relates to a method for the treatment of cancer in a patient in need thereof. The method comprises administering to a patient in need thereof a first amount of a histone deacetylase inhibitor and a second amount or dose of radiation in a second treatment procedure. The first and second amounts together comprise a therapeutically effective amount.

[0053] In one embodiment, the method provides an anticancer effect which is synergistic.

[0054] Treatment of cancer, as used herein, refers to partially or totally inhibiting, delaying or preventing the progression of cancer including cancer metastasis; inhibiting, delaying or preventing the recurrence of cancer including cancer metastasis; or preventing the onset or development of cancer (chemoprevention) in a mammal, for example a human.

[0055] In one embodiment, the HDAC inhibitor sensitizes cancer cells in the patient to radiation. As such, the HDAC inhibitor can act as a radiosensitizer. For example, without wishing to be bound to any particular mechanism or theory, the therapeutic effect of the combination administration of an HDAC inhibitor and a radiation treatment can be due to the ability of the HDAC inhibitor to act as a radiosensitizer, thereby increasing the sensitivity of cancer cells in the patients to the radiation treatment. As such, the HDAC inhibitor can be administered in a radiosensitizing amount. The sensitization can be due to an irreversible arrest in cell cycling.

[0056] In another embodiment, the radiation sensitizes cancer cells in the patient to the action of the HDAC inhibitor.

[0057] The invention also relates to a method of determining the sensitivity of a particular cancer to the combination therapy of the invention. The method comprises exposing or contacting a cancer cell with a first amount of a histone deacetylase inhibitor in a first treatment procedure, and a second amount or dose of radiation in a second treatment procedure and assessing the anticancer effects. The first and second amounts together comprise a therapeutically effective amount. The anticancer effects can be assessed using any suitable assay.

[0058] In a further embodiment, the invention relates to a method of screening to determine optimum combinations of HDAC inhibitors and radiation therapy for particular cancer types. The method of screening comprises exposing a cancer cell to a first amount of a histone deacetylase inhibitor in a first treatment procedure, and a second amount or dose of radiation in a second treatment procedure. The first and second treatments together comprise a therapeutically effective amount. The cell can be in culture or present in the body of the patient in need of treatment. The anticancer effects of the treatment can be assessed using suitable methods.

[0059] As used herein the term “therapeutically effective amount” is intended to qualify the combined amount of the first and second treatments in the combination therapy. The combined amount will achieve the desired biological response. In the present invention, the desired biological response is partial or total inhibition, delay or prevention of the progression of cancer including cancer metastasis; inhibition, delay or prevention of the recurrence of cancer including cancer metastasis; or the prevention of the onset or development of cancer (chemoprevention) in a mammal, for example a human.

[0060] The combination therapy of the present invention is suitable for use in the treatment of a wide variety of cancers. As used herein, cancer refers to tumors, neoplasms, carcinomas, sarcomas, leukemias, lymphomas and the like. For example, cancers include, but are not limited to, leukemias and lymphomas such as cutaneous T-cell lymphoma (CTCL), noncutaneous peripheral T-cell lymphoma, lymphomas associated with human T-cell lymphotropic virus (HTLV), for example, adult T-cell leukemia/lymphoma (ATLL), acute lymphocytic leukemia, acute nonlymphocytic leukemias, chronic lymphocytic leukemia, chronic myelogenous leukemia, Hodgkin's Disease, non-Hodgkin's lymphomas, and multiple myeloma, childhood solid tumors such as brain tumors, neuroblastoma, retinoblastoma, Wilms' Tumor, bone tumors, and soft-tissue sarcomas, common solid tumors of adults such as head and neck cancers (e.g., oral, laryngeal and esophageal), genitourinary cancers (e.g., prostate, bladder, renal, uterine, ovarian, testicular, rectal and colon), lung cancer, breast cancer, pancreatic cancer, melanoma and other skin cancers, stomach cancer, brain cancer, liver cancer and thyroid cancer.

[0061] Histone Deacetylases and Histone Deacetylase Inhibitors

[0062] Histone deacetylases (HDACs) as that term is used herein are enzymes which catalyze the removal of acetyl groups from lysine residues in the amino terminal tails of the nucleosomal core histones. As such, HDACs together with histone acetyl transferases (HATs) regulate the acetylation status of histones. Histone acetylation affects gene expression and inhibitors of HDACs, such as the hydroxamic acid-based hybrid polar compound suberoylanilide hydroxamic acid (SAHA) induce growth arrest, differentiation and/or apoptosis of transformed cells in vitro and inhibit tumor growth in vivo. HDACs can be divided into three classes based on structural homology. Class I HDACs (HDACs 1, 2, 3 and 8) bear similarity to the yeast RPD3 protein, are located in the nucleus and are found in complexes associated with transcriptional co-repressors. Class II HDACs (HDACs 4, 5, 6, 7 and 9) are similar to the yeast HDA1 protein, and have both nuclear and cytoplasmic subcellular localization. Both Class I and II HDACs are inhibited by hydroxamic acid-based HDAC inhibitors, such as SAHA. Class III HDACs form a structurally distant class of NAD dependent enzymes that are related to the yeast SIR2 proteins and are not inhibited by hydroxamic acid-based HDAC inhibitors.

[0063] Histone deacetylase inhibitors or HDAC inhibitors, as that term is used herein are compounds which are capable of inhibiting the deacetylation of histones in vivo, in vitro or both. As such, HDAC inhibitors inhibit the activity of at least one histone deacetylase. As a result of inhibiting the deacetylation of at least one histone, an increase in acetylated histone occurs and accumulation of acetylated histone is a suitable biological marker for assessing the activity of HDAC inhibitors. Therefore, procedures which can assay for the accumulation of acetylated histones can be used to determine the HDAC inhibitory activity of compounds of interest. It is understood that compounds which can inhibit histone deacetylase activity can also bind to other substrates and as such can inhibit other biologically active molecules such as enzymes.

[0064] For example, in patients receiving HDAC inhibitors, the accumulation of acetylated histones in peripheral mononuclear cells as well as in tissue treated with HDAC inhibitors can be determined against a suitable control.

[0065] HDAC inhibitory activity of a particular compound can be determined in vitro using, for example, an enzymatic assays which shows inhibition of at least one histone deacetylase. Further, determination of the accumulation of acetylated histones in cells treated with a particular composition can be determinative of the HDAC inhibitory activity of a compound.

[0066] Assays for the accumulation of acetylated histones are well known in the literature. See, for example, Marks, P. A. et al., J. Natl. Cancer Inst., 92:1210-1215, 2000, Butler, L. M. et al., Cancer Res. 60:5165-5170 (2000), Richon, V. M. et al., Proc. Natl. Acad. Sci., USA, 95:3003-3007, 1998, and Yoshida, M. et al., J. Biol. Chem., 265:17174-17179, 1990.

[0067] For example, an enzymatic assay to determine the activity of a histone deacetylase inhibitor compound can be conducted as follows. Briefly, the effect of an HDAC inhibitor compound on affinity purified human epitope-tagged (Flag) HDAC1 can be assayed by incubating the enzyme preparation in the absence of substrate on under suitable temperatures for about 20 minutes with the indicated amount of inhibitor compound. Substrate ([ 3 H]acetyl-labelled murine erythroleukemia cell-derived histone) can be added and the sample can be incubated for 20 minutes at about 37° C. in a total volume of 30 μL. The reaction can then be stopped and released acetate can be extracted and the amount of radioactivity released determined by scintillation counting. An alternative assay useful for determining the activity of a histone deacetylase inhibitor compound is the “HDAC Fluorescent Activity Assay; Drug Discovery Kit-AK-500” available from BIOMOL® Research Laboratories, Inc., Plymouth Meeting, Pa.

[0068] In vivo studies can be conducted as follows. Animals, for example mice, can be injected intraperitoneally with an HDAC inhibitor compound. Selected tissues, for example brain, spleen, liver etc, can be isolated at predetermined times, post administration. Histones can be isolated from tissues essentially as described by Yoshida et al., J. Biol. Chem. 265:17174-17179, 1990. Equal amounts of histones (about 1 μg) can be electrophoresed on 15% SDS-polyacrylamide gels and can be transferred to Hybond-P filters (available from Amersham). Filters can be blocked with 3% milk and can be probed with a rabbit purified polyclonal anti-acetylated histone H4 antibody (αAc-H4) and anti-acetylated histone H3 antibody (αAc-H3) (Upstate Biotechnology, Inc.). Levels of acetylated histone can be visualized using a horseradish peroxidase-conjugated goat anti-rabbit antibody (1:5000) and the SuperSignal chemiluminescent substrate (Pierce). As a loading control for the histone protein, parallel gels can be run and stained with Coomassie Blue (CB).

[0069] In addition, hydroxamic acid-based HDAC inhibitors like SAHA have been shown to up regulate the expression of the p21 WAF1 gene, responsible for the inhibition of cyclin-dependent kinases that contributes to a transient arrest in the G 1 phase of the cell-cycle (Richon, V. M. et al. Proc Natl Acad Sci USA. 97: 10014-9., 2000). The p21 WAF1 protein is induced within 2 hours of culture with HDAC inhibitors in a variety of transformed cells using standard methods. The induction of the p21 WAF1 gene is associated with accumulation of acetylated histones in the chromatin region of this gene. Induction of p21 WAF1 can therefore be recognized as involved in the G 1 cell cycle arrest caused by HDAC inhibitors in transformed cells.

[0070] Recently it has been shown that HDAC inhibitors like SAHA up-regulate thioredoxin-binding protein-2 (Butler, L. M. et al. Proc Natl Acad Sci USA. 99: 11700-5., 2002). TBP-2 is involved in the regulation of thioredoxin (Nishiyama, A. et al. J Biol Chem. 274: 21645-50., 1999). It inhibits the thiol reducing activity and reduces the level of thioredoxin. Thioredoxin is a major cellular protein disulfide reductase (Arner, E. S. et al. Eur J Biochem. 267: 6102-9., 2000). In addition to a number of other functions (Gasdaska, J. R. et al. Cell Growth Differ. 6: 1643-50., 1995; Berggren, M. et al. Anticancer Res. 16: 3459-66., 1996; Gallegos, A. et al. Cancer Res. 56: 5765-70., 1996; Grogan, T. M. et al. Hum Pathol. 31: 475-81., 2000; Baker, A. et al. Cancer Res. 57: 5162-7., 1997), thioredoxin serves as an electron donor in the ribonucleotide reductase reaction that is responsible for the reduction of nucleoside triphosphates to deoxynucleoside triphosphates needed in DNA replication and repair (Amer, E. S. et al. Eur J Biochem. 267: 6102-9., 2000). Like glutathione, thioredoxin is also a reducing agent involved in detoxification reactions and in the elimination of radiation-induced reactive oxygen species and other free radicals (Didier, C. et al. P Radic Biol Med. 30: 537-46., 2001).

[0071] As such, hydroxamic acid derivatives, such as SAHA, are suitable for use in treating or preventing a wide variety of thioredoxin (TRX)-mediated diseases and conditions, such as inflammatory diseases, allergic diseases, autoimmune diseases, diseases associated with oxidative stress or diseases characterized by cellular hyperproliferation (U.S. application No. Ser. 10/369,094, filed Feb. 15, 2003, entitled, “Method of treating TRX-mediated diseases using histone deacetylase inhibitors” by Richon et al., the entire content of which is hereby incorporated by reference).

[0072] Further, hydroxamic acid derivatives, such as SAHA, have recently been shown to be useful for treating diseases of the central nervous system (CNS), such as neurodegenerative diseases and for treating brain cancer (U.S. application Ser. No. 10/273,401, filed Oct. 16, 2002, entitled “Treatment of neurodegenerative diseases and cancer of the brain using histone deacetylase inhibitors” by Richon et al., the entire content of which is hereby incorporated by reference).

[0073] Typically, HDAC inhibitors fall into five general classes: 1) hydroxamic acid derivatives; 2) Short-Chain Fatty Acids (SCFAs); 3) cyclic tetrapeptides; 4) benzamides; and 5) electrophilic ketones.

[0074] Thus, all HDAC inhibitor compounds are suitable for use in the present invention. For example, suitable HDAC inhibitors include 1) hydroxamic acid derivatives; 2) Short-Chain Fatty Acids (SCFAs); 3) cyclic tetrapeptides; 4) benzamides; 5) electrophilic ketones; and/or any other class of compounds capable of inhibiting histone deacetylase.

[0075] Examples of such HDAC inhibitors include, but are not limited to:

[0076] A) HYDROXAMIC ACID DERIVATIVES such as Suberoylanilide Hydroxamic Acid (SAHA) (Richon et al., Proc. Natl. Acad. Sci. USA 95,3003-3007 (1998)); M-Carboxycinnamic Acid Bishydroxamide (CBHA) (Richon et al., supra); pyroxamide; CBHA; Trichostatin analogues such as Trichostatin A (TSA) and Trichostatin C (Koghe et al. 1998. Biochem. Pharmacol. 56: 1359-1364); Salicylihydroxamic Acid (SBHA) (Andrews et al., International J. Parasitology 30,761-768 (2000)); Azelaic Bishydroxamic Acid (ABHA) (Andrews et al., supra); Azelaic-1-Hydroxamate-9-Anilide (AAHA) (Qiu et al., Mol. Biol. Cell 11, 2069-2083 (2000)); 6-(3-Chlorophenylureido) carpoic Hydroxamic Acid (3Cl-UCHA), Oxamflatin [(2E)-5-[3-[(phenylsuibnyl)amino phenyl]-pent-2-en-4-ynohydroxamic acid (Kim et al. Oncogene, 18: 2461 2470 (1999)); A-161906, Scriptaid (Su et al. 2000 Cancer Research, 60: 3137-3142); PXD-101 (Prolifix); LAQ-824; CHAP; MW2796 (Andrews et al., supra); and MW2996 (Andrews et al., supra).

[0077] B) CYCLIC TETRAPEPTIDES such as Trapoxin A (TPX)-Cyclic Tetrapeptide (cyclo-(L-phenylalanyl-L-phenylalanyl-D-pipecolinyl-L-2-amin o-8-oxo-9,10-epoxy decanoyl)) (Kijima et al., J Biol. Chem. 268,22429-22435 (1993)); FR901228 (FK 228, Depsipeptide) (Nakajima et al., Ex. Cell Res. 241,126-133 (1998)); FR225497 Cyclic Tetrapeptide (H. Mori et al., PCT Application WO 00/08048 (Feb. 17, 2000));, Apicidin Cyclic Tetrapeptide [cyclo (NO-methyl-L-tryptophanyl-L-isoleucinyl-D-pipecolinyl-L-2-am ino-8oxodecanoyl)] (Darkin-Rattray et al., Proc. Natl. Acad. Sci. USA 93,1314313147 (1996)); Apicidin la, Apicidin Ib, Apicidin Ic, Apicidin IIa, and Apicidin IIb (P. Dulski et al., PCT Application WO 97/11366); CHAP, HC-Toxin Cyclic Tetrapeptide (Bosch et al., Plant Cell 7, 1941-1950 (1995)); WF27082 Cyclic Tetrapeptide (PCT Application WO 98/48825); and Chiamydocin (Bosch et al., supra).

[0078] C) SHORT CHAIN FATTY ACID (SCFA) DERIVATIVES such as: Sodium Butyrate (Cousens et al., J. Biol. Chem. 254,1716-1723 (1979)); Isovalerate (McBain et al., Biochem. Pharm. 53: 1357-1368 (1997)); Valerate (McBain et al., supra); 4 Phenylbutyrate (4-PBA) (Lea and Tulsyan, Anticancer Research, 15,879-873 (1995)); Phenylbutyrate (PB) (Wang et al., Cancer Research, 59, 2766-2799 (1999)); Propionate (McBain et al., supra); Butyramide (Lea and Tulsyan, supra); Isobutyramide (Lea and Tulsyan, supra); Phenylacetate (Lea and Tulsyan, supra); 3-Bromopropionate (Lea and Tulsyan, supra); Tributyrin (Guan et al., Cancer Research, 60,749-755 (2000)); Valproic acid and Valproate.

[0079] D) BENZAMIDE DERIVATIVES such as CI-994; MS-27-275 [N-(2-aminophenyl)-4-[N-(pyridin-3-ylmethoxycarbonyl)aminome thyl]benzamide] (Saito et al., Proc. Natl. Acad. Sci. USA 96, 4592-4597 (1999)); and 3′-amino derivative of MS-27-275 (Saito et al., supra).

[0080] E) ELECTROPHILIC KETONE DERIVATIVES such as trifluoromethyl ketones (Frey et al, Bioorganic & Med. Chem. Lett. (2002), 12, 3443-3447; U.S. 6,511,990) and α-keto amides such as N-methyl-α-ketoamides

[0081] F) OTHER HDAC Inhibitors such as Depudecin (Kwon et al. 1998. PNAS 95: 3356-3361.

[0082] Preferred hydroxamic acid based HDAC inhibitors are suberoylanilide hydroxamic acid (SAHA), m-carboxycinnamic acid bishydroxamate (CBHA) and pyroxamide. SAHA has been shown to bind directly in the catalytic pocket of the histone deacetylase enzyme. SAHA induces cell cycle arrest, differentiation and/or apoptosis of transformed cells in culture and inhibits tumor growth in rodents. SAHA is effective at inducing these effects in both solid tumors and hematological cancers. It has been shown that SAHA is effective at inhibiting tumor growth in animals with no toxicity to the animal. The SAHA-induced inhibition of tumor growth is associated with an accumulation of acetylated histones in the tumor. SAHA is effective at inhibiting the development and continued growth of carcinogen-induced (N-methylnitrosourea) mammary tumors in rats. SAHA was administered to the rats in their diet over the 130 days of the study. Thus, SAHA is a nontoxic, orally active antitumor agent whose mechanism of action involves the inhibition of histone deacetylase activity.

[0083] SAHA can be represented by the following structural formula: 7

[0084] Pyroxamide can be represented by the following structural formula: 8

[0085] CBHA can be represented by the structural formula: 9

[0086] In one embodiment, the HDAC inhibitor can be represented by Formula I: 10

[0087] wherein R 1 and R 2 can be the same or different; when R 1 and R 2 are the same, each is a substituted or unsubstituted arylamino (e.g., pyridineamino, 9-purine-6-amino or thiazoleamino), cycloalkylamino or piperidino group; when R 1 and R 2 are different R 1 ═R 3 —N—R 4 , wherein each of R 3 and R 4 are independently the same as or different from each other and are a hydrogen atom, a hydroxyl group, a substituted or unsubstituted, branched or unbranched alkyl, alkenyl, cycloalkyl, aryl, alkyloxy, aryloxy, arylalkyloxy group, or R 3 and R 4 are bonded together to form a piperidine group, R 2 is a hydroxylamino, hydroxyl, amino, alkylamino, dialkylamino or alkyloxy group and n is an integer from about 4 to about 8.

[0088] As such, in another embodiment the HDAC inhibitors used in the method of the invention can be represented by Formula II: 11

[0089] wherein each of R 3 and R 4 are independently the same as or different from each other and are a hydrogen atom, a hydroxyl group, a substituted or unsubstituted, branched or unbranched alkyl, alkenyl, cycloalkyl, aryl, alkyloxy, aryloxy or arylalkyloxy group, or R 3 and R 4 are bonded together to form a piperidine group, R 2 is a hydroxylamino, hydroxyl, amino, alkylamino, dialkylamino or alkyloxy group and n is an integer from about 4 to about 8.

[0090] In a particular embodiment of Formula II, R 2 is a hydroxylamino, hydroxyl, amino, methylamino, dimethylamino or methyloxy group and n is 6. In yet another embodiment of Formula II, R 4 is a hydrogen atom, R 3 is a substituted or unsubstituted phenyl and n is 6. In further embodiments of Formula II, R 4 is hydrogen and R 3 is an α-, β-, or γ-pyridine.

[0091] In other specific embodiments of Formula II, R 4 is a hydrogen atom and R 3 is a cyclohexyl group; R 4 is a hydrogen atom and R 3 is a methoxy group; R 3 and R 4 each bond together to form a piperidine group; R 4 is a hydrogen atom and R 3 is a hydroxyl group; R 3 and R 4 are both a methyl group and R 3 is phenyl and R 4 is methyl.

[0092] Further HDAC inhibitors suitable for use in the present invention can be represented by structural Formula III: 12

[0093] wherein each of X and Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino, or aryloxyalkylamino group; R is a hydrogen atom, a hydroxyl, group, a substituted or unsubstituted alkyl, arylalkyloxy, or aryloxy group; and each of m and n are independently the same as or different from each other and are each an integer from about 0 to about 8.

[0094] In a particular embodiment, the HDAC inhibitor is a compound of Formula III wherein X, Y and R are each hydroxyl and both m and n are 5.

[0095] In yet another embodiment, the HDAC inhibitor compounds suitable for use in the method of the invention can be represented by structural Formula IV: 13

[0096] wherein each of X and Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino or aryloxyalkylamino group; each of R 1 and R 2 are independently the same as or different from each other and are a hydrogen atom, a hydroxyl group, a substituted or unsubstituted alkyl, aryl, alkyloxy, or aryloxy group; and each of m, n and o are independently the same as or different from each other and are each an integer from about 0 to about 8.

[0097] Other HDAC inhibitors suitable for use in the invention include compounds having structural Formula V: 14

[0098] wherein each of X and Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino or aryloxyalkylamino group; each of R 1 and R 2 are independently the same as or different from each other and are a hydrogen atom, a hydroxyl group, a substituted or unsubstituted alkyl, aryl, alkyloxy, or aryloxy group; and each of m and n are independently the same as or different from each other and are each an integer from about 0 to about 8.

[0099] In a further embodiment, HDAC inhibitors suitable for use in the method of the present invention can have structural Formula VI: 15

[0100] wherein each of X and Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino or aryloxyalkylamino group; and each of m and n are independently the same as or different from each other and are each an integer from about 0 to about 8.

[0101] In yet another embodiment, the HDAC inhibitors useful in the method of the invention can have structural Formula VII: 16

[0102] wherein each of X and Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino or aryloxyalkylamino group; R 1 and R 2 are independently the same as or different from each other and are a hydrogen atom, a hydroxyl group, a substituted or unsubstituted alkyl, arylalkyloxy or aryloxy group; and each of m and n are independently the same as or different from each other and are each an integer from about 0 to about 8.

[0103] In yet a further embodiment, HDAC inhibitors suitable for use in the invention can have structural Formula VIII: 17

[0104] wherein each of X an Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, or aryloxyalkylamino group; and n is an integer from about 0 to about 8.

[0105] Additional compounds suitable for use in the method of the invention include those represented by Formula IX: 18

[0106] wherein Each of X and Y are independently the same as or different from each other and are a hydroxyl, amino or hydroxylamino group, a substituted or unsubstituted alkyloxy, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino or aryloxyalkylamino group; each of R 1 and R 2 are independently the same as or different from each other and are a hydrogen atom, a hydroxyl group, a substituted or unsubstituted alkyl, aryl, alkyloxy, aryloxy, carbonylhydroxylamino or fluoro group; and each of m and n are independently the same as or different from each other and are each an integer from about 0 to about 8.

[0107] In a further embodiment, HDAC inhibitors suitable for use in the invention include compounds having structural Formula X: 19

[0108] wherein each of R 1 and R 2 are independently the same as or different from each other and are a hydroxyl, alkyloxy, amino, hydroxylamino, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino, or aryloxyalkylamino group. In a particular embodiment, the HDAC inhibitor is a compound of structural Formula X wherein R 1 and R 2 are both hydroxylamino. In a further embodiment, the HDAC inhibitor suitable for use in the invention has structural Formula XI: 20

[0109] wherein each of R 1 and R 2 are independently the same as or different from each other and are a hydroxyl, alkyloxy, amino, hydroxylamino, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino, or aryloxyalkylamino group. In a particular embodiment, the HDAC inhibitor is a compound of structural Formula XI wherein R 1 and R 2 are both hydroxylamino.

[0110] In a further embodiment, HDAC inhibitors suitable for use in the present invention include compounds represented by structural Formula XII: 21

[0111] wherein each of R 1 and R 2 are independently the same as or different from each other and are a hydroxyl, alkyloxy, amino, hydroxylamino, alkylamino, dialkylamino, arylamino, alkylarylamino, alkyloxyamino, aryloxyamino, alkyloxyalkylamino, or aryloxyalkylamino group. In a particular embodiment, the HDAC inhibitor is a compound of structural Formula XII wherein R 1 and R 2 are both hydroxylamino.

[0112] Additional compounds suitable for use in the method of the invention include those represented by structural Formula XIII: 22

[0113] wherein R is a substituted or unsubstituted phenyl, piperidine, thiazole, 2-pyridine, 3-pyridine or 4-pyridine and n is an integer from about 4 to about 8.

[0114] In yet another embodiment, the HDAC inhibitors suitable for use in the method of the invention can be represented by structural Formula (XIV): 23

[0115] wherein R is a substituted or unsubstituted phenyl, pyridine, piperidine or thiazole group and n is an integer from about 4 to about 8 or a pharmaceutically acceptable salt thereof.

[0116] In a particular embodiment, R is phenyl and n is 5. In another embodiment, n is 5 and R is 3-chlorophenyl.

[0117] Other HDAC inhibitors useful in the present invention can be represented by structural Formula XV: 24

[0118] wherein each of R 1 and R 2 is directly attached or through a linker and is a hydroxyl, substituted or unsubstituted, aryl (e.g. naphthyl, phenyl, quinolinyl, isoquinolinyl or pyridyl), cycloalkyl, cycloalkylamino, piperidino, branched or unbranched alkyl, alkenyl, arylamino (pyridineamino, 9-purine-6-amino or thiazoleamino), arylalkylamino, arylalkyl, alkyloxy, aryloxy or arylalkoxy group; n is an integer from about 3 to about 10 and R 3 is a hydroxamic acid, hydroxylamino, hydroxyl, amino, alkylamino or alkyloxy group.

[0119] The linker can be an amide moiety, —O—, —S—, —NH— or —CH2—.

[0120] In certain embodiments, R 1 is —NH—R 4 wherein R 4 is a hydroxyl, substituted or unsubstituted, aryl (e.g., naphthyl, phenyl, quinolinyl, isoquinolinyl or pyridyl), cycloalkyl, cycloalkylamino, piperidino, branched or unbranched alkyl, alkenyl, arylamino (e.g., pyridineamino, 9-purine-6-amine or thiazoleamino), arylalkylamino, alkyloxy, arylalkyl, aryloxy or arylalkyloxy group.

[0121] Further and more specific HDAC inhibitors of Formula XV, include those which can be represented by Formula XVI: 25

[0122] wherein each of R 1 and R 2 is hydroxyl, substituted or unsubstituted, aryl (e.g., phenyl, naphthyl, quinolinyl, isoquinolinyl or pyridyl), cycloalkyl, cycloalkylamino, piperidino, arylamino (e.g., pyridineamino, 9-purine-6-amino or thiazoleamino), arylalkylamino, branched or unbranched alkyl, alkenyl, alkyloxy, arylalkyl, aryloxy or arylalkyloxy group; R 3 is hydroxamic acid, hydroxylamino, hydroxyl, amino, alkylamino or alkyloxy group; R 4 is hydrogen, halogen, phenyl or a cycloalkyl moiety; and A can be the same or different and represents an amide moiety, —O—, —S—, —NR 5 — or —CH 2 — where R 5 is a substituted or unsubstituted C 1 -C 5 alkyl and n is an integer from about 3 to about 10.

[0123] For example, further compounds having a more specific structure within Formula XVI can be represented by structural Formula XVII: 26

[0124] wherein A is an amide moiety, R 1 and R 2 are each selected from substituted or unsubstituted aryl (e.g., phenyl, naphthyl, quinolinyl, isoquinolinyl or pyridyl), arylamino (e.g., pyridineamino, 9-purine-6-amine or thiazoleamino), arylalkylamino, arylalkyl, aryloxy or arylalkyloxy group and n is an integer from about 3 to about 10.

[0125] For example, compounds having an amide moiety at A can be represented by the formula: 27

[0126] In another embodiment, the HDAC inhibitor can have the Formula XVIII: 28

[0127] wherein R 7 is selected from substituted or unsubstituted aryl (e.g., phenyl, naphthyl, quinolinyl, isoquinolinyl or pyridyl), arylamino (e.g., pyridineamino, 9-purine-6-amine or thiazoleamino), arylalkylamino, arylalkyl, aryloxy or arylalkyloxy and n is an integer from about 3 to about 10 and Y is selected from 29

[0128] or a pharmaceutically acceptable salt thereof.

[0129] In a further embodiment, the HDAC inhibitor compound can have Formula XIX: 30

[0130] wherein n is an integer from about 3 to about 10, Y is selected from 31

[0131] and R 7 ′ is selected from 32

[0132] or a pharmaceutically acceptable salt thereof.

[0133] Further compounds for use in the invention can be represented by structural Formula XX: 33

[0134] wherein R 2 is selected from a substituted or unsubstituted aryl, arylamino (e.g., pyridineamino, 9-purine-6-amino or thiazoleamino), arylalkylamino, arylalkyl or aryloxy, arylalkyloxy group and n is an integer from 3 to 10 and R 7 ′ is selected from 34

[0135] Further HDAC inhibitors useful in the invention can be represented by structural Formula XXI: 35

[0136] wherein A is an amide moiety, R 1 and R 2 are each selected from a substituted or unsubstituted aryl, arylamino (e.g., pyridineamino, 9-purine-6-amine or thiazoleamino) arylalkylamino, arylalkyl, aryloxy or arylalkyloxy group, R 4 is hydrogen, a halogen, a phenyl or a cycloalkyl moiety and n is an integer from about 3 to about 10 or a pharmaceutically acceptable salt thereof.

[0137] For example, a compound of Formula XXI can be represented by the structure: 36

[0138] or can be represented by the structure: 37

[0139] wherein R 1 , R 2 , R 4 and n have the meanings of Formula XXI. Further, HDAC inhibitors having the structural Formula XXII: 38

[0140] wherein L is a linker selected from the group consisting of —(CH2) n —, —(CH═CH) m , phenyl, -cycloalkyl-, or any combination thereof; and wherein each of R 7 and R 8 are independently substituted or unsubstituted, aryl, arylamino (e.g., pyridineamino, 9-purine-6-amino or thiazoleamino), arylalkylamino, arylalkyl, aryloxy or arylalkyloxy group, n is an integer from about 3 to about 10 and m is an integer from 0-10.

[0141] For example, a compound of Formula XXII can be: 39

[0142] Other HDAC inhibitors suitable for use in the invention include those shown in the following more specific formulas: 40

[0143] wherein n is an integer from 3 to 10 or an enantiomer or, 41

[0144] wherein n is an integer from 3 to 10 or an enantiomer or 42

[0145] wherein n is an integer from 3 to 10 or an enantiomer or 43

[0146] wherein n is an integer from 3 to 10 or an enantiomer or 44

[0147] wherein n is an integer from 3 to 10 or an enantiomer.

[0148] Further specific HDAC inhibitors suitable for use in the invention include 45

[0149] wherein n in each is an integer from 3 to 10 and the compound 46

[0150] Further specific HDAC inhibitors of include those which can be represented by Formula XXIII: 47

[0151] wherein R 1 is a substituted or unsubstituted aryl group, arylalkyl group, arylamino group, arylalkylamino group, aryloxy group or arylalkoxy group and n is an integer from 3 to 10. In a particular embodiment, n is 5 for the compounds of Structural Formula XXIII.

[0152] In a specific embodiment, the compound of Formula XXIII is represented by the following structure: 48

[0153] In another specific embodiment, the compound of Formula XXIII is represented by the following structure: 49

[0154] In yet another specific embodiment, the compound of Formula XXIII is represented by the following structure: 50

[0155] In still another specific embodiment, the compound of Formula XXIII is represented by the following structure: 51

[0156] Further specific HDAC inhibitors include those which can be represented by Formula XXIV: 52

[0157] wherein Q 1 is a substituted or unsubstituted quinolinyl or isoquinolinyl group and n is an integer from 3 to 10. In a particular embodiment, n is 5 for the compounds of Structural Formula XXIV.

[0158] In a specific embodiment, the compound of Formula XXIV is represented by the following structure: 53

[0159] Further specific HDAC inhibitors include those which can be represented by Formula XXV: 54

[0160] wherein Q 1 and Q 2 are independently a substituted or unsubstituted quinolinyl or isoquinolinyl group and n is an integer from about 3 to about 10. In a particular embodiment, n is 5 for the compounds of Structural Formula XXV.

[0161] In a specific embodiment, the compound of Formula XXV is represented by the following structure: 55

[0162] Further specific HDAC inhibitors include those which can be represented by Formula XXVI: 56

[0163] wherein R 1 is an arylalkyl, R 2 is a substituted or unsubstituted aryl group, arylalkyl group, arylamino group, arylalkylamino group, aryloxy group or arylalkoxy group, A is an amide and n is an integer from 3 to 10. In a particular embodiment, n is 5 for the compounds of Structural Formula XXVI.

[0164] In a specific embodiment, the compound of Formula XXVI is represented by the following structure: 57

[0165] In a specific embodiment, the compound of Formula XXVI is represented by the following structure: 58

[0166] In a specific embodiment, the compound of Formula XXVI is represented by the following structure: 59

[0167] Other examples of such compounds and other HDAC inhibitors can be found in U.S. Pat. Nos. 5,369,108, issued on Nov. 29, 1994, 5,700,811, issued on Dec. 23, 1997, 5,773,474, issued on Jun. 30, 1998, 5,932,616 issued on Aug. 3, 1999 and 6,511,990, issued Jan. 28, 2003 all to Breslow et al.; U.S. Pat. Nos. 5,055,608, issued on Oct. 8, 1991, 5,175,191, issued on Dec. 29, 1992 and 5,608,108, issued on Mar. 4, 1997 all to Marks et al.; U.S. Provisional Application No. 60/459,826, filed Apr. 1, 2003 in the name of Breslow et al.; as well as, Yoshida, M., et al., Bioassays 17, 423-430 (1995); Saito, A., et al., PNAS USA 96, 4592-4597, (1999); Furamai R. et al., PNAS USA 98 (1), 87-92 (2001); Komatsu, Y., et al., Cancer Res. 61(11), 4459-4466 (2001); Su, G. H., et al., Cancer Res. 60, 3137-3142 (2000); Lee, B. I. et al., Cancer Res. 61(3), 931-934; Suzuki, T., et al., J. Med. Chem. 42(15), 3001-3003 (1999); published PCT Application WO 01/18171 published on Mar. 15, 2001 Sloan-Kettering Institute for Cancer Research and The Trustees of Columbia University; published PCT Application WO02/246144 to Hoffmann-La Roche; published PCT Application WO02/22577 to Novartis; published PCT Application WO02/30879 to Prolifix; published PCT Applications WO 01/38322 (published May 31, 2001), WO 01/70675 (published on Sep. 27, 2001) and WO 00/71703 (published on Nov. 30, 2000) all to Methylgene, Inc.; published PCT Application WO 00/21979 published on Oct. 8, 1999 to Fujisawa Pharmaceutical Co., Ltd.; published PCT Application WO 98/40080 published on Mar. 11, 1998 to Beacon Laboratories, L.L.C.; and Curtin M. (Current patent status of histone deacetylase inhibitors Expert Opin. Ther. Patents (2002) 12(9): 1375-1384 and references cited therein).

[0168] Specific non-limiting examples of HDAC inhibitors are provided in the Table below. It should be noted that the present invention encompasses any compounds which are structurally similar to the compounds represented below, and which are capable of inhibiting histone deacetylases. 1

Title
MS-275	60
DEPSIPEPTIDE	61
CI-994	62
Apicidin	63
A-161906	64
Scriptaid	65
PXD-101	66
CHAP	67
LAQ-824	68
Butyric Acid	69
Depudecin	70
Oxamflatin	71
Trichostatin C	72

[0169] Definitions

[0170] An “aliphatic group” is non-aromatic, consists solely of carbon and hydrogen and can optionally contain one or more units of unsaturation, e.g., double and/or triple bonds. An aliphatic group can be straight chained, branched or cyclic. When straight chained or branched, an aliphatic group typically contains between about 1 and about 12 carbon atoms, more typically between about 1 and about 6 carbon atoms. When cyclic, an aliphatic group typically contains between about 3 and about 10 carbon atoms, more typically between about 3 and about 7 carbon atoms. Aliphatic groups are preferably C 1 -C 12 straight chained or branched alkyl groups (i.e., completely saturated aliphatic groups), more preferably C 1 -C 6 straight chained or branched alkyl groups. Examples include methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl and tert-butyl.

[0171] An “aromatic group” (also referred to as an “aryl group”) as used herein includes carbocyclic aromatic groups, heterocyclic aromatic groups (also referred to as “heteroaryl”) and fused polycyclic aromatic ring system as defined herein.

[0172] A “carbocyclic aromatic group” is an aromatic ring of 5 to 14 carbons atoms, and includes a carbocyclic aromatic group fused with a 5-or 6-membered cycloalkyl group such as indan. Examples of carbocyclic aromatic groups include, but are not limited to, phenyl, naphthyl, e.g., 1-naphthyl and 2-naphthyl; anthracenyl, e.g., 1-anthracenyl, 2-anthracenyl; phenanthrenyl; fluorenonyl, e.g., 9-fluorenonyl, indanyl and the like. A carbocyclic aromatic group is optionally substituted with a designated number of substituents, described below.

[0173] A “heterocyclic aromatic group” (or “heteroaryl”) is a monocyclic, bicyclic or tricyclic aromatic ring of 5- to 14-ring atoms of carbon and from one to four heteroatoms selected from O, N, or S. Examples of heteroaryl include, but are not limited to pyridyl, e.g., 2-pyridyl (also referred to as “α-pyridyl), 3-pyridyl (also referred to as β-pyridyl) and 4-pyridyl (also referred to as (γ-pyridyl); thienyl, e.g., 2-thienyl and 3-thienyl; furanyl, e.g., 2-furanyl and 3-furanyl; pyrimidyl, e.g., 2-pyrimidyl and 4-pyrimidyl; imidazolyl, e.g., 2-imidazolyl