HISTONE DEACETYLASE INHIBITORS

In recognition of the need to develop novel therapeutic agents, the present invention provides novel histone deacetylase inhibitors. These compounds include an ester bond making them sensitive to deactivation by esterases. Therefore, these compounds are particularly useful in the treatment of skin disorders. When the compounds reaches the bloodstream, an esterase or an enzyme with esterase activity cleaves the compound into biologically inactive fragments or fragments with greatly reduced activity Ideally these degradation products exhibit a short serum and/or systemic half-life and are eliminated rapidly. These compounds and pharmaceutical compositions thereof are particularly useful in treating cutaneous T-cell lymphoma, neurofibromatosis, psoriasis, hair loss, skin pigmentation, and dermatitis, for example. The present invention also provides methods for preparing compounds of the invention and intermediates thereto.

DETAILED DESCRIPTION OF THE INVENTION

As discussed above, there remains a need for the development of novel histone deacetylase inhibitors. The present invention provides novel compounds of general formula (I), and methods for the synthesis thereof, which compounds are useful as inhibitors of histone deacetylases, and thus are useful for the treatment of proliferative diseases, particularly proliferative or other disorders associated with the skin and/or hair. In particular, the inventive compounds comprise an ester linkage. The ester linkage is preferably sensitive to esterase cleavage; therefore, when the compound is contacted with an esterase it is deactivated.

Compounds of the Invention

As discussed above, the present invention provides a novel class of compounds useful for the treatment of cancer and other proliferative conditions related thereto. In certain embodiments, the compounds of the present invention are useful as inhibitors of histone deacetylases and thus are useful as anticancer agents, and thus may be useful in the treatment of cancer, by effecting tumor cell death or inhibiting the growth of tumor cells. In certain exemplary embodiments, the inventive anticancer agents are useful in the treatment of cancers and other proliferative disorders, including, but not limited to breast cancer, cervical cancer, colon and rectal cancer, leukemia, lung cancer, melanoma, multiple myeloma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, and gastric cancer, to name a few. In certain embodiments, the inventive anticancer agents are active against leukemia cells and melanoma cells, and thus are useful for the treatment of leukemias (e.g., myeloid, lymphocytic, myelocytic and lymphoblastic leukemias) and malignant melanomas. In certain embodiments, the inventive compounds are active against cutaneous T-cell lymphoma. Additionally, as described above and in the exemplification, the inventive compounds may also be useful in the treatment of protozoal infections. In certain exemplary embodiments, the compounds of the invention are useful for disorders resulting from histone deacetylation activity. In certain embodiments, the compounds are useful for skin disorders. Examplary skin disorders that may be treated using the inventive compounds include cutaneous T-cell lymphoma (CTCL), skin cancers (e.g., squamous cell carcinoma, basal cell carcinoma, malignant melanoma, etc.), psoriasis, hair loss, dermatitis, neurofibromatosis, disorders asscoiated with skin hyperpigmentation, etc.

Compounds of this invention comprise those, as set forth above and described herein, and are illustrated in part by the various classes, subgenera and species disclosed elsewhere herein.

In general, the present invention provides compounds having the general structure (I):

and pharmaceutically acceptable salts and derivatives thereof;
wherein

A comprises a functional group that inhibits histone deacetylase;

L is a linker moiety; and

Ar is a substituted or unsubstituted aryl or heteroaryl moiety; substituted or unsustituted, branched or unbranched arylaliphatic or heteroarylaliphatic moiety; a substituted or unsubstituted cyclic or heterocyclic moiety; substituted or unsustituted, branched or unbranched cyclicaliphatic or heterocyclicaliphatic moiety.

In certain embodiments, A comprises a metal chelating functional group. For example, A comprises a Zn2+chelating group. In certain embodiments, A comprises a functional group selected group consisting of:

In certain embodiments, A comprises hydroxamic acid

or a salt thereof. In other embodiments, A comprises the formula:

In certain particular embodiments, A comprises the formula:

In other embodiments, A comprises a carboxylic acid (—CO2H). In other embodiments, A comprises an o-aminoanilide

In other embodiments, A comprises an o-hydroxyanilide

In yet other embodiments, A comprises a thiol (—SH).

In certain embodiments, Ar is arylaliphatic. In other embodiments, Ar is heteroarylaliphatic. In certain embodiments, Ar is a substituted or unsubstituted aryl moiety. In certain embodiments, Ar is a monocylic, substituted or unsubstituted aryl moiety, preferably a five- or six-membered aryl moiety. In other embodiments, Ar is a bicyclic, substituted or unsubstituted aryl moiety. In still other embodiments, Ar is a tricyclic, substituted or unsubstituted aryl moiety. In certain embodiments, Ar is a susbstituted or unsubstituted phenyl moiety. In certain embodiments, Ar is an unsubstituted phenyl moiety. In other embodiments, Ar is a substituted phenyl moiety. In certain embodiments, Ar is a monosubstituted phenyl moiety. In certain particular embodiments, Ar is an ortho-substituted Ar moiety. In certain particular embodiments, Ar is an meta-substituted Ar moiety. In certain particular embodiments, Ar is an para-substituted Ar moiety. In certain embodiments, Ar is a disubstituted phenyl moiety. In certain embodiments, Ar is a trisubstituted phenyl moiety. In certain embodiments, Ar is a tetrasubstituted phenyl moiety. In certain embodiments, Ar is a substituted or unsubstituted cyclic or heterocyclic.

In certain embodiments, Ar is a substituted or unsubstituted heteroaryl moiety. In certain embodiments, Ar is a monocylic, substituted or unsubstituted heteroaryl moiety, preferably a five- or six-membered heteroaryl moiety. In other embodiments, Ar is a bicyclic, substituted or unsubstituted heteroaryl moiety. In still other embodiments, Ar is a tricyclic, substituted or unsubstituted heteroaryl moiety. In certain embodiments, Ar comprises N, S, or O. In certain embodiments, Ar comprises at least one N. In certain embodiments, Ar comprises at least two N.

In certain embodiments, Ar is:

wherein

n is an integer between 1 and 5, inclusive; preferably, between 1 and 3, inclusive; more preferably, 1 or 2;

In other embodiments, Ar is

In yet other embodiments, Ar is

In certain particular embodiments, Ar is a substituted phenyl moiety of formula:

In certain embodiments, Ar is chosen from one of the following:

wherein

n is an integer between 1 and 4, inclusive; preferably, between 1 and 3, inclusive; more preferably, 1 or 2;

In certain embodiments, Ar is chosen from one of the following:

Any of the above bicyclic ring system may be substituted with up to seven R1susbstituents as defined above.

In certain embodiments, L is a substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic moiety; a substituted or unsubstituted, cyclic or acyclic, branched or unbranched heteroaliphatic moiety; a substituted or unsubstituted aryl moiety; a substituted or unsubstituted heteroaryl moiety. In certain embodiments, L is a substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic moiety. In certain embodiments, L is C1-C20alkylidene, preferably C1to C12alkylidene, more preferably C4-C7alkylidene. In certain embodiments, L is C1-C20alkenylidene, preferably C1to C12alkenylidene, more preferably C4-C7alkenylidene. In certain embodiments, L is C1-C20alkynylidene, preferably C1to C12alkynylidene, more preferably C4-C7alkynylidene. In certain embodiments, L is a a substituted or unsubstituted, cyclic or acyclic, branched or unbranched heteroaliphatic moiety. In certain embodiments, L comprises a cyclic ring system, wherein the rings may be aryl, heteroaryl, non-aromatic carbocyclic, or non-aromatic heterocyclic. In still other embodiments, L comprises a substituted or unsubstituted heteroaryl moiety. In certain particular embodiments, L comprises a phenyl ring. In certain embodiments, L comprises multiple phenyl rings (e.g., one, two, three, or four phenyl rings).

In certain embodiments, L is

In certain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclic alkyl chain. In certain embodiments, L is

In other embodiments, L is

In certain other embodiments, L is

In other embodiments, L is

In yet other embodiments, L is

In certain embodiments, L is a substituted, acyclic aliphatic chain. In certain embodiments, L is

In certain embodiments, L is an unbranched, unsubstituted, acyclic heteroaliphatic chain. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive; and m is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive; and m is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive; m is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive; and R′ is hydrogen, C1-C6aliphatic, heteroaliphatic, aryl, heteroaryl, or acyl. In certain particular embodiments, L is

wherein n is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive; and m is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive.

In certain embodiments of the invention, compounds of formula (I) have the following structure as shown in formula (Ia):

wherein

Ar is defined as above. In certain embodiments, n is 5. In other embodiments, n is 6. In still other embodiments, n is 7.

In certain embodiments of the invention, compounds of formula (I) have the following structure as shown in formula (Ib):

wherein

m is an integer between 1 and 5, inclusive; preferably, m is 1, 2, or 3; and

In certain embodiments of the invention, compounds of formula (I) are of the formula (Ic):

wherein

In certain embodiments of the invention, compounds of formula (I) are of the formula (Id):

wherein

n is an integer between 1 and 5, inclusive; preferably, between 1 and 3; more preferably, 1 or 2; and

In certain embodiments of the invention, compounds of formula (I) are of the formula (Ie):

wherein R1 is defined as above.

In certain embodiments of the invention, compounds of formula (I) have the following stereochemistry and structure as shown in formula (If):

wherein A, L and Ar are defined as above; and

n is an integer between 0 and 10, inclusive; preferably, between 0 and 5, inclusive; even more preferably, 0, 1, 2, or 3. In certain embodiments, Ar is phenyl.

In certain embodiments, compounds of formula (I) are of the formula (Ig):

wherein

A and L are defined as above;

In certain embodiments, R2is hydrogen. In other embodiments, R2is hydroxyl or a protected hydroxyl group. In certain embodiments, R2is alkoxy. In yet other embodiments, R2is a lower alkyl, alkenyl, or alkynyl group. In certain embodiments, R2is —CH2—X(RB)n, wherein X is O, S, N, or C, preferably O, S, or N; and n is 1, 2, or 3. In certain embodiments, R2is —CH2—ORB. In other embodiments, R2is —CH2—SRB. In yet other embodiments, R2is —CH2—RB. In other embodiments, R2is —CH2—N(RB)2. In still other embodiments, R2is —CH2—NHRB. In certain embodiments of the invention, RBis one of:

wherein m and p are each independently integers from 0 to 3; q1is an integer from 1 to 6; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety. In certain embodiments of the invention, RBis one of the structures:

wherein m is an integer from 1 to 4; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(RB)nhas one of the structures:

In certain embodiments, R2is

wherein X is N and Y is NH, S, or O. In other embodiments, R2is

In other embodiments, R3is substituted or unsubstituted heteroaryl.

In certain embodiments, the stereochemistry of formula (Ig) is defined as follows:

In certain embodiments of the invention, compounds of formula (I) are of the formula (Ih):

wherein

A and L are defined as above;

n is an integer between 0 and 10, inclusive; preferably, between 1 and 6, inclusive; more preferably, between 1 and 3, inclusive; and even more preferably, 0, 1, 2, or 3;

In certain embodiments, R2is hydrogen. In other embodiments, R2is hydroxyl or a protected hydroxyl group. In certain embodiments, R2is alkoxy. In yet other embodiments, R2is a lower alkyl, alkenyl, or alkynyl group. In certain embodiments, R2is —CH2—X(RB)n, wherein X is O, S, N, or C, preferably O, S, or N; and n is 1, 2, or 3. In certain embodiments, R2is —CH2—ORB. In other embodiments, R2is —CH2—SRB. In yet other embodiments, R2is —CH2—RB. In other embodiments, R2is —CH2—N(RB)2. In still other embodiments, R2is —CH2—NHRB. In certain embodiments of the invention, RBis one of:

wherein m and p are each independently integers from 0 to 3; q1is an integer from 1 to 6; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety. In certain embodiments of the invention, RBis one of the structures:

wherein m is an integer from 1 to 4; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(RB)nhas one of the structures:

In certain embodiments, R2is

wherein X is N and Y is NH, S, or O. In other embodiments, R2is

In other embodiments, R3is substituted or unsubstituted heteroaryl.

In certain embodiments, the stereochemistry of formula (Ih) is defined as follows:

In certain embodiments of the invention, compounds of formula (I) have structure as shown in formula (Ii):

wherein

A and L are defined as above;

In certain embodiments, R2is hydrogen. In other embodiments, R2is hydroxyl or a protected hydroxyl group. In certain embodiments, R2is alkoxy. In yet other embodiments, R2is a lower alkyl, alkenyl, or alkynyl group. In certain embodiments, R2is —CH2—X(RB)n, wherein X is O, S, N, or C, preferably O, S, or N; and n is 1, 2, or 3. In certain embodiments, R2is —CH2—ORB. In other embodiments, R2is —CH2—SRB. In yet other embodiments, R2is —CH2—RB. In other embodiments, R2is —CH2—N(RB)2. In still other embodiments, R2is —CH2—NHRB. In certain embodiments of the invention, RBis one of:

wherein m and p are each independently integers from 0 to 3; q1is an integer from 1 to 6; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety. In certain embodiments of the invention, RBis one of the structures:

wherein m is an integer from 1 to 4; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(RB)nhas one of the structures:

In certain embodiments, R2is

wherein X is N and Y is NH, S, or O. In other embodiments, R2is

In other embodiments, R3is substituted or unsubstituted heteroaryl.

In certain embodiments, the stereochemistry of formula (II) is defined as follows:

In certain embodiments of the invention, compounds of formula (I) have the following stereochemistry and structure as shown in formula (Ij):

wherein

In certain embodiments, R2is hydrogen. In other embodiments, R2is hydroxyl or a protected hydroxyl group. In certain embodiments, R2is alkoxy. In yet other embodiments, R2is a lower alkyl, alkenyl, or alkynyl group. In certain embodiments, R2is —CH2—X(RB)n, wherein X is O, S, N, or C, preferably O, S, or N; and n is 1, 2, or 3. In certain embodiments, R2is —CH2—ORB. In other embodiments, R2is —CH2—SRB. In yet other embodiments, R2is —CH2—RB. In other embodiments, R2is —CH2—N(RB)2. In still other embodiments, R2is —CH2—NHRB. In certain embodiments of the invention, RBis one of:

wherein m and p are each independently integers from 0 to 3; q1is an integer from 1 to 6; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety. In certain embodiments of the invention, RBis one of the structures:

wherein m is an integer from 1 to 4; R2Cis hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2Bis independently hydrogen, halogen, —CN, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety.

In certain embodiments, —X(RB)nhas one of the structures:

In certain embodiments, R2is

wherein X is N and Y is NH, S, or O. In other embodiments, R2is

In other embodiments, R3is substituted or unsubstituted heteroaryl.

Another class of compounds of special interest includes those compounds of the invention as described above and in certain subclasses herein, wherein R3is a substituted phenyl moiety and the compounds have the formula (Il):

wherein

n is an integer between 0 and 5, inclusive; preferably, between, 1 and 3; more preferably, 2; and

Another class of compounds includes those compounds of formula (II), wherein Z is —CH2ORZ, and the compounds have the general structure (Im):

wherein

RB, RZ, X, L, n, and A are defined generally above and in classes and subclasses herein. In certain embodiments, X is S. In other embodiments, X is O.

Yet another class of compounds of particular interest includes those compounds of formula (Ii), wherein X is S and the compounds have the general structure (In):

wherein

RB, X, L, n, and A are defined as above; and

RZis as defined generally above and in classes and subclasses herein.

Yet another class of compounds of special interest includes those compounds of formula (Ii), wherein X is —NR2Aand the compounds have the general structure (Io):

wherein

RB, RZ, X, L, n, and A are defined generally above and in classes and subclasses herein.

Yet another class of compounds of special interest includes those compounds of formula (Ii), wherein X is O and the compounds have the general structure (Ip):

wherein

RB, RZ, X, L, n, and A are defined generally above and in classes and subclasses herein.

Exemplary compounds of the invention are shown:

Some of the foregoing compounds can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., stereoisomers and/or diastereomers. Thus, inventive compounds and pharmaceutical compositions thereof may be in the form of an individual enantiomer, diastereomer or geometric isomer, or may be in the form of a mixture of stereoisomers. In certain embodiments, the compounds of the invention are enantiopure compounds. In certain other embodiments, mixtures of stereoisomers or diastereomers are provided.

Furthermore, certain compounds, as described herein may have one or more double bonds that can exist as either the Z or E isomer, unless otherwise indicated. The invention additionally encompasses the compounds as individual isomers substantially free of other isomers and alternatively, as mixtures of various isomers, e.g., racemic mixtures of stereoisomers. In addition to the above-mentioned compounds per se, this invention also encompasses pharmaceutically acceptable derivatives of these compounds and compositions comprising one or more compounds of the invention and one or more pharmaceutically acceptable excipients or additives.

Compounds of the invention may be prepared by crystallization of the compound under different conditions and may exist as one or a combination of polymorphs of the compound forming part of this invention. For example, different polymorphs may be identified and/or prepared using different solvents, or different mixtures of solvents for recrystallization; by performing crystallizations at different temperatures; or by using various modes of cooling, ranging from very fast to very slow cooling during crystallizations. Polymorphs may also be obtained by heating or melting the compound followed by gradual or fast cooling. The presence of polymorphs may be determined by solid probe NMR spectroscopy, IR spectroscopy, differential scanning calorimetry, powder X-ray diffractogram and/or other techniques. Thus, the present invention encompasses inventive compounds, their derivatives, their tautomeric forms, their stereoisomers, their polymorphs, their pharmaceutically acceptable salts their pharmaceutically acceptable solvates and pharmaceutically acceptable compositions containing them.

Synthetic Overview

The synthesis of the various monomeric compounds used to prepare the dimeric, multimeric, and polymeric compounds of the invention are known in the art. These published syntheses may be utilized to prepare the compounds of the invention. Exemplary synthesic methods for preparing compounds of the invention are described in U.S. Pat. No. 6,960,685; U.S. Pat. No. 6,897,220; U.S. Pat. No. 6,541,661; U.S. Pat. No. 6,512,123; U.S. Pat. No. 6,495,719; US 2006/0020131; US 2004/087631; US 2004/127522; US 2004/0072849; US 2003/0187027; WO 2005/018578; WO 2005/007091; WO 2005/007091; WO 2005/018578; WO 2004/046104; WO 2002/89782; each of which is incorporated herein by reference. In many cases, an amide moiety is changed to an ester moiety to prepare the inventive compounds.

An exemplary synthetic scheme for preparing SAHP is showin inFIG. 13. Those of skill in the art will realize that based on this teaching and those in the art as referenced above one could prepare any of the esterase-sensitive compounds of the invention.

In yet another aspect of the invention, methods for producing intermediates useful for the preparation of certain compounds of the invention are provided.

In one aspect of the invention, a method for the synthesis of the core structure of certain compounds is provided, one method comprising steps of:

providing an epoxy alcohol having the structure:

reacting the epoxy alcohol with a reagent having the structure R2XH under suitable conditions to generate a diol having the core structure:

reacting the diol with a reagent having the structure R3CH(OMe)2under suitable conditions to generate a scaffold having the core structure:

or wherein two or more occurrences of R2and R2A, taken together, form an alicyclic or heterocyclic moiety, or an aryl or heteroaryl moiety;

RZis an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic or heteroaromatic moiety and is optionally attached to a solid support.

In certain exemplary embodiments, the epoxy alcohol has the structure:

the diol has the structure:

and the core scaffold has the structure:

In certain other exemplary embodiments, the epoxy alcohol has the structure:

the diol has the structure:

and the core scaffold has the structure:

In certain embodiments, R3has the following structure:

and the method described above generates the structure:

In another aspect of the invention, a method for the synthesis of the core structure of certain compounds of the invention is provided, one method comprising steps of:

providing an epoxy alcohol having the structure:

reacting the epoxy alcohol with a reagent having the structure R2XH under suitable conditions to generate a diol having the core structure:

subjecting the diol to a reagent having the structure:

wherein R4Cis a nitrogen protecting group; to suitable conditions to generate an amine having the structure:

reacting the amine with a reagent having the structure:

under suitable conditions to generate a scaffold having the core structure:

or wherein two or more occurrences of R2and R2A, taken together, form an alicyclic or heterocyclic moiety, or an aryl or heteroaryl moiety;

r is 0 or 1;

s is an integer from 2-5;

w is an integer from 0-4;

R4Acomprises a metal chelator;

each occurrence of R4Dis independently hydrogen, alkyl, heteroalkyl, cycloalkyl, heterocyclic, alkenyl, alkynyl, aryl, heteroaryl, halogen, CN, NO2, or WRW1wherein W is O, S, NRW2, —C(═O), —S(═O), —SO2, —C(═O)O—, —OC(═O), —C(═O)NRW2, —NRW2C(═O); wherein each occurrence of RW1and RW2is independently hydrogen, a protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1and RW2, taken together with the nitrogen atom to which they are attached, form a heterocyclic or heteroaryl moiety; or any two adjacent occurrences of R2B, taken together with the atoms to which they are attached, form a substituted or unsubstituted, saturated or unsaturated alicyclic or heterocyclic moiety, or a substituted or unsubstituted aryl or heteroaryl moiety; and

RZis an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aromatic or heteroaromatic moiety and is optionally attached to a solid support.

In certain exemplary embodiments, the epoxy alcohol has the structure:

the diol has the structure:

the amine has the structure:

and the core scaffold has the structure:

In certain exemplary embodiments, the epoxy alcohol has the structure:

the diol has the structure:

the amine has the structure:

and the core scaffold has the structure:

In certain embodiments, the methods described above are carried out in solution phase. In certain other embodiments, the methods described above are carried out on a solid phase. In certain embodiments, the synthetic method is amenable to high-throughput techniques or to techniques commonly used in combinatorial chemistry.

Pharmaceutical Compositions

As discussed above, the present invention provides novel compounds having antitumor and antiproliferative activity, and thus the inventive compounds are useful for the treatment of cancer (e.g., cutaneous T-cell lymphoma). Benign proliferative diseases may also be treated using the inventive compounds. The compounds are also useful in the treatment of other diseases or condition that benefit from inhibtion of deacetylation activity (e.g. HDAC inhibition). In certain embodiments, the compounds are useful in the treatment of baldness based on the discovery that HDAC inhibition (particularly, HDAC6 inhibition) blocks androgen signaling vis hsp90. HDAC inhibition has also been shown to inhibit estrogen signaling. In certain embodiments, the compounds are useful in blocking the hyperpigmentation of skin by HDAC inhibition.

Accordingly, in another aspect of the present invention, pharmaceutical compositions are provided, which comprise any one of the compounds described herein (or a prodrug, pharmaceutically acceptable salt or other pharmaceutically acceptable derivative thereof), and optionally comprise a pharmaceutically acceptable carrier. In certain embodiments, these compositions optionally further comprise one or more additional therapeutic agents. Alternatively, a compound of this invention may be administered to a patient in need thereof in combination with the administration of one or more other therapeutic agents. For example, additional therapeutic agents for conjoint administration or inclusion in a pharmaceutical composition with a compound of this invention may be an approved chemotherapeutic agent, or it may be any one of a number of agents undergoing approval in the Food and Drug Administration that ultimately obtain approval for the treatment of hair loss, skin hyperpigmentation, protozoal infections, and/or any disorder associated with cellular hyperproliferation. In certain other embodiments, the additional therapeutic agent is an anticancer agent, as discussed in more detail herein. In certain other embodiments, the compositions of the invention are useful for the treatment of protozoal infections.

It will also be appreciated that certain of the compounds of present invention can exist in free form for treatment, or where appropriate, as a pharmaceutically acceptable derivative thereof. According to the present invention, a pharmaceutically acceptable derivative includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or a pro-drug or other adduct or derivative of a compound of this invention which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.

Furthermore, the term “pharmaceutically acceptable prodrugs” as used herein refers to those prodrugs of the compounds of the present invention which are, within the scope of sound medical judgment, suitable for use in contact with the issues of humans and lower animals with undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the invention. The term “prodrug” refers to compounds that are rapidly transformed in vivo to yield the parent compound of the above formula, for example by hydrolysis in blood. A thorough discussion is provided in T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series, and in Edward B. Roche, ed., Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press, 1987, both of which are incorporated herein by reference.

As described above, the pharmaceutical compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, which, as used herein, includes any and all solvents, diluents, or other liquid vehicle, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980) discloses various carriers used in formulating pharmaceutical compositions and known techniques for the preparation thereof. Except insofar as any conventional carrier medium is incompatible with the compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutical composition, its use is contemplated to be within the scope of this invention. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatine; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil, sesame oil; olive oil; corn oil and soybean oil; glycols; such as propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogenfree water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.

The present invention encompasses pharmaceutically acceptable topical formulations of inventive compounds. The term “pharmaceutically acceptable topical formulation”, as used herein, means any formulation which is pharmaceutically acceptable for intradermal administration of a compound of the invention by application of the formulation to the epidermis. In certain embodiments of the invention, the topical formulation comprises a carrier system. Pharmaceutically effective carriers include, but are not limited to, solvents (e.g., alcohols, poly alcohols, water), creams, lotions, ointments, oils, plasters, liposomes, powders, emulsions, microemulsions, and buffered solutions (e.g., hypotonic or buffered saline) or any other carrier known in the art for topically administering pharmaceuticals. A more complete listing of art-known carriers is provided by reference texts that are standard in the art, for example,Remington's Pharmaceutical Sciences,16th Edition, 1980 and 17th Edition, 1985, both published by Mack Publishing Company, Easton, Pa., the disclosures of which are incorporated herein by reference in their entireties. In certain other embodiments, the topical formulations of the invention may comprise excipients. Any pharmaceutically acceptable excipient known in the art may be used to prepare the inventive pharmaceutically acceptable topical formulations. Examples of excipients that can be included in the topical formulations of the invention include, but are not limited to, preservatives, antioxidants, moisturizers, emollients, buffering agents, solubilizing agents, other penetration agents, skin protectants, surfactants, and propellants, and/or additional therapeutic agents used in combination to the inventive compound. Suitable preservatives include, but are not limited to, alcohols, quaternary amines, organic acids, parabens, and phenols. Suitable antioxidants include, but are not limited to, ascorbic acid and its esters, sodium bisulfite, butylated hydroxytoluene, butylated hydroxyanisole, tocopherols, and chelating agents like EDTA and citric acid. Suitable moisturizers include, but are not limited to, glycerine, sorbitol, polyethylene glycols, urea, and propylene glycol. Suitable buffering agents for use with the invention include, but are not limited to, citric, hydrochloric, and lactic acid buffers. Suitable solubilizing agents include, but are not limited to, quaternary ammonium chlorides, cyclodextrins, benzyl benzoate, lecithin, and polysorbates. Suitable skin protectants that can be used in the topical formulations of the invention include, but are not limited to, vitamin E oil, allatoin, dimethicone, glycerin, petrolatum, and zinc oxide.

In certain embodiments, the pharmaceutically acceptable topical formulations of the invention comprise at least a compound of the invention and a penetration enhancing agent. The choice of topical formulation will depend or several factors, including the condition to be treated, the physicochemical characteristics of the inventive compound and other excipients present, their stability in the formulation, available manufacturing equipment, and costs constraints. As used herein the term “penetration enhancing agent” means an agent capable of transporting a pharmacologically active compound through the stratum corneum and into the epidermis or dermis, preferably, with little or no systemic absorption. A wide variety of compounds have been evaluated as to their effectiveness in enhancing the rate of penetration of drugs through the skin. See, for example,Percutaneous Penetration Enhancers, Maibach H. I. and Smith H. E. (eds.), CRC Press, Inc., Boca Raton, Fla. (1995), which surveys the use and testing of various skin penetration enhancers, and Buyuktimkin et al., Chemical Means of Transdermal Drug Permeation Enhancement in Transdermal and Topical Drug Delivery Systems, Gosh T. K., Pfister W. R., Yum S. I. (Eds.), Interpharm Press Inc., Buffalo Grove, Ill. (1997). In certain exemplary embodiments, penetration agents for use with the invention include, but are not limited to, triglycerides (e.g., soybean oil), aloe compositions (e.g., aloe-vera gel), ethyl alcohol, isopropyl alcohol, octolyphenylpolyethylene glycol, oleic acid, polyethylene glycol 400, propylene glycol, N-decylmethylsulfoxide, fatty acid esters (e.g., isopropyl myristate, methyl laurate, glycerol monooleate, and propylene glycol monooleate), and N-methylpyrrolidone.

In certain embodiments, the compositions may be in the form of ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. In certain exemplary embodiments, formulations of the compositions according to the invention are creams, which may further contain saturated or unsaturated fatty acids such as stearic acid, palmitic acid, oleic acid, palmito-oleic acid, cetyl or oleyl alcohols, stearic acid being particularly preferred. Creams of the invention may also contain a non-ionic surfactant, for example, polyoxy-40-stearate. In certain embodiments, the active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, eardrops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms are made by dissolving or dispensing the compound in the proper medium. As discussed above, penetration enhancing agents can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

It will also be appreciated that the compounds and pharmaceutical compositions of the present invention can be formulated and employed in combination therapies, that is, the compounds and pharmaceutical compositions can be formulated with or administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another immunomodulatory agent, anticancer agent or agent useful for the treatment of psoriasis), or they may achieve different effects (e.g., control of any adverse effects).

For example, other therapies or anticancer agents that may be used in combination with the inventive compounds of the present invention include surgery, radiotherapy (in but a few examples, γ-radiation, neutron beam radiotherapy, electron beam radiotherapy, proton therapy, brachytherapy, and systemic radioactive isotopes, to name a few), endocrine therapy, biologic response modifiers (interferons, interleukins, and tumor necrosis factor (TNF) to name a few), hyperthermia and cryotherapy, agents to attenuate any adverse effects (e.g., antiemetics), and other approved chemotherapeutic drugs, including, but not limited to, alkylating drugs (mechlorethamine, chlorambucil, Cyclophosphamide, Melphalan, Ifosfamide), antimetabolites (Methotrexate), purine antagonists and pyrimidine antagonists (6-Mercaptopurine, 5-Fluorouracil, Cytarabile, Gemcitabine), spindle poisons (Vinblastine, Vincristine, Vinorelbine, Paclitaxel), podophyllotoxins (Etoposide, Irinotecan, Topotecan), antibiotics (Doxorubicin, Bleomycin, Mitomycin), nitrosoureas (Carmustine, Lomustine), inorganic ions (Cisplatin, Carboplatin), enzymes (Asparaginase), and hormones (Tamoxifen, Leuprolide, Flutamide, and Megestrol), to name a few. For a more comprehensive discussion of updated cancer therapies see,The Merck Manual, Seventeenth Ed. 1999, the entire contents of which are hereby incorporated by reference. See also the National Cancer Institute (CNI) website (www.nci.nih.gov) and the Food and Drug Administration (FDA) website for a list of the FDA approved oncology drugs (www.fda.gov/cder/cancer/druglistframe).

In certain embodiments, the pharmaceutical compositions of the present invention further comprise one or more additional therapeutically active ingredients (e.g., chemotherapeutic and/or palliative). For purposes of the invention, the term “palliative” refers to treatment that is focused on the relief of symptoms of a disease and/or side effects of a therapeutic regimen, but is not curative. For example, palliative treatment encompasses painkillers, antinausea medications and anti-sickness drugs. In addition, chemotherapy, radiotherapy and surgery can all be used palliatively (that is, to reduce symptoms without going for cure; e.g., for shrinking tumors and reducing pressure, bleeding, pain and other symptoms of cancer).

Additionally, the present invention provides pharmaceutically acceptable derivatives of the inventive compounds, and methods of treating a subject using these compounds, pharmaceutical compositions thereof, or either of these in combination with one or more additional therapeutic agents.

It will also be appreciated that certain of the compounds of present invention can exist in free form for treatment, or where appropriate, as a pharmaceutically acceptable derivative thereof. According to the present invention, a pharmaceutically acceptable derivative includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or a prodrug or other adduct or derivative of a compound of this invention which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof.

Research Uses, Pharmaceutical Uses and Methods of Treatment

Research Uses

According to the present invention, the inventive compounds may be assayed in any of the available assays known in the art for identifying compounds having antiprotozoal, HDAC inhibitory, hair growth, androgen signalling inhibitory, estogen singaling inhibitory, and/or antiproliferative activity. For example, the assay may be cellular or non-cellular, in vivo or in vitro, high- or low-throughput format, etc.

Thus, in one aspect, compounds of this invention which are of particular interest include those which:exhibit HDAC-inhibitory activity;exhibit HDAC Class I inhbitiory activity (e.g., HDAC1, HDAC2, HDAC3, HDAC8);exhibit HDAC Class II inhibitory activity (e.g., HDAC4, HDAC5, HDAC6, HDAC7, HDAC9a, HDAC9b, HDRP/HDAC9c, HDAC10);exhibit the ability to inhibit HDAC1 (Genbank Accession No. NP—004955, incorporated herein by reference);exhibit the ability to inhibit HDAC2 (Genbank Accession No. NP—001518, incorporated herein by reference);exhibit the ability to inhibit HDAC3 (Genbank Accession No. O15739, incorporated herein by reference);exhibit the ability to inhibit HDAC4 (Genbank Accession No. AAD29046, incorporated herein by reference);exhibit the ability to inhibit HDAC5 (Genbank Accession No. NP—005465, incorporated herein by reference);exhibit the ability to inhibit HDAC6 (Genbank Accession No. NP—006035, incorporated herein by reference);exhibit the ability to inhibit HDAC7 (Genbank Accession No. AAP63491, incorporated herein by reference);exhibit the ability to inhibit HDAC8 (Genbank Accession No. AAF73428, NM—018486, AF245664, AF230097, each of which is incorporated herein by reference);exhibit the ability to inhibit HDAC9 (Genbank Accession No. NM—178425, NM—178423, NM—058176, NM—014707, BC111735, NM—058177, each of which is incorporated herein by reference)exhibit the ability to inhibit HDAC10 (Genbank Accession No. NM—032019, incorporated herein by reference)exhibit the ability to inhibit HDAC11 (Genbank Accession No. BC009676, incorporated herein by reference);exhibit the ability to inhibit tubulin deactetylation (TDAC);exhibit the ability to modulate the glucose-sensitive subset of genes downstream of Ure2p;exhibit cytotoxic or growth inhibitory effect on cancer cell lines maintained in vitro or in animal studies using a scientifically acceptable cancer cell xenograft model; and/orexhibit a therapeutic profile (e.g., optimum safety and curative effect) that is superior to existing chemotherapeutic agents.

As detailed in the exemplification herein, in assays to determine the ability of compounds to inhibit cancer cell growth certain inventive compounds may exhibit IC50values ≦100 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦50 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦40 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦30 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦20 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦10 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦7.5 μM. In certain embodiments, inventive compounds exhibit IC50values ≦5 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦2.5 μM. In certain embodiments, inventive compounds exhibit IC50values ≦1 μM. In certain embodiments, inventive compounds exhibit IC50values ≦0.75 μM. In certain embodiments, inventive compounds exhibit IC50values ≦0.5 μM. In certain embodiments, inventive compounds exhibit IC50values ≦0.25 μM. In certain embodiments, inventive compounds exhibit IC50values ≦0.1 μM. In certain other embodiments, inventive compounds exhibit IC50values ≦75 nM. In certain other embodiments, inventive compounds exhibit IC50values ≦50 nM. In certain other embodiments, inventive compounds exhibit IC50values ≦25 nM. In certain other embodiments, inventive compounds exhibit IC50values ≦10 nM. In other embodiments, exemplary compounds exhibited IC50values ≦7.5 nM. In other embodiments, exemplary compounds exhibited IC50values ≦5 nM.

Pharmaceutical Uses and Methods of Treatment

In general, methods of using the compounds of the present invention comprise administering to a subject in need thereof a therapeutically effective amount of a compound of the present invention. The compounds of the invention are generally inhibitors of deacetyalse activity. As discussed above, the compounds of the invention are typically inhibitors of histone deacetylases and, as such, are useful in the treatment of disorders modulated by histone deacetylases. Other deacetylase such as tubulin deacetylases may also be inhibited by the inventive compounds.

In certain embodiments, compounds of the invention are useful in the treatment of proliferative diseases (e.g., cancer, benign neoplasms, inflammatory disease, autoimmune diseases). In certain embodiments, given the esterase sensitive ester linkage in the compounds of the invention, they are particularly useful in treating skin disorders modulated by histone deacetyalses where systemic effects of the drug are to be avoided or at least minimized. This feature of the inventive compounds may allow the use of compounds normally too toxic for administration to a subject systemically. In certain embodiments, these skin disorders are proliferative disorders. For example, the inventive compounds are particularly useful in the treatment of skin cancer and benign skin tumors. In certain embodiments, the compounds are useful in the treatment of cutaneous T-cell lymphoma. In certain embodiments, the compounds are useful in the treatment of neurofibromatosis. Accordingly, in yet another aspect, according to the methods of treatment of the present invention, tumor cells are killed, or their growth is inhibited by contacting said tumor cells with an inventive compound or composition, as described herein. In other embodiments, the compounds are useful in treating inflammatory diseases of the skin such as psoriasis or dermatitis. In other embodiments, the compounds are useful in the treatment or prevention of hair loss. In certain embodiments, the compounds are useful in the treatment of diseases associated with skin pigmentation. For example, the compounds may be used to prevent the hyperpigmentation of skin.

Thus, in another aspect of the invention, methods for the treatment of cancer are provided comprising administering a therapeutically effective amount of an inventive compound, as described herein, to a subject in need thereof. In certain embodiments, a method for the treatment of cancer is provided comprising administering a therapeutically effective amount of an inventive compound, or a pharmaceutical composition comprising an inventive compound to a subject in need thereof, in such amounts and for such time as is necessary to achieve the desired result. Preferably, the inventive compounds is administered topically. In certain embodiments of the present invention a “therapeutically effective amount” of the inventive compound or pharmaceutical composition is that amount effective for killing or inhibiting the growth of tumor cells. The compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for killing or inhibiting the growth of tumor cells. Thus, the expression “amount effective to kill or inhibit the growth of tumor cells,” as used herein, refers to a sufficient amount of agent to kill or inhibit the growth of tumor cells. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular anticancer agent, its mode of administration, and the like. In certain embodiments of the present invention a “therapeutically effective amount” of the inventive compound or pharmaceutical composition is that amount effective for inhibiting deacetylase activity (in particular, HDAC activity) in skin cells. In certain embodiments of the present invention a “therapeutically effective amount” of the inventive compound or pharmaceutical composition is that amount effective to kill or inhibit the growth of skin cells.

In certain embodiments, the method involves the administration of a therapeutically effective amount of the compound or a pharmaceutically acceptable derivative thereof to a subject (including, but not limited to a human or animal) in need of it. In certain embodiments, the inventive compounds as useful for the treatment of cancer (including, but not limited to, glioblastoma, retinoblastoma, breast cancer, cervical cancer, colon and rectal cancer, leukemia, lymphoma, lung cancer (including, but not limited to small cell lung cancer), melanoma and/or skin cancer, multiple myeloma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer and gastric cancer, bladder cancer, uterine cancer, kidney cancer, testicular cancer, stomach cancer, brain cancer, liver cancer, or esophageal cancer).

In certain embodiments, the inventive anticancer agents are useful in the treatment of cancers and other proliferative disorders, including, but not limited to breast cancer, cervical cancer, colon and rectal cancer, leukemia, lung cancer, melanoma, multiple myeloma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, and gastric cancer, to name a few. In certain embodiments, the inventive anticancer agents are active against leukemia cells and melanoma cells, and thus are useful for the treatment of leukemias (e.g., myeloid, lymphocytic, myelocytic and lymphoblastic leukemias) and malignant melanomas. In still other embodiments, the inventive anticancer agents are active against solid tumors.

In certain embodiments, the inventive compounds also find use in the prevention of restenosis of blood vessels subject to traumas such as angioplasty and stenting. For example, it is contemplated that the compounds of the invention will be useful as a coating for implanted medical devices, such as tubings, shunts, catheters, artificial implants, pins, electrical implants such as pacemakers, and especially for arterial or venous stents, including balloon-expandable stents. In certain embodiments inventive compounds may be bound to an implantable medical device, or alternatively, may be passively adsorbed to the surface of the implantable device. In certain other embodiments, the inventive compounds may be formulated to be contained within, or, adapted to release by a surgical or medical device or implant, such as, for example, stents, sutures, indwelling catheters, prosthesis, and the like. For example, drugs having antiproliferative and anti-inflammatory activities have been evaluated as stent coatings, and have shown promise in preventing retenosis (See, for example, Presbitero P. et al., “Drug eluting stents do they make the difference?”,Minerva Cardioangiol,2002, 50(5):431-442; Ruygrok P. N. et al., “Rapamycin in cardiovascular medicine”,Intern. Med. J.,2003, 33(3):103-109; and Marx S. O. et al., “Bench to bedside: the development of rapamycin and its application to stent restenosis”,Circulation,2001, 104(8):852-855, each of these references is incorporated herein by reference in its entirety). Accordingly, without wishing to be bound to any particular theory, Applicant proposes that inventive compounds having antiproliferative effects can be used as stent coatings and/or in stent drug delivery devices, inter alia for the prevention of restenosis or reduction of restenosis rate. Suitable coatings and the general preparation of coated implantable devices are described in U.S. Pat. Nos. 6,099,562; 5,886,026; and 5,304,121. The coatings are typically biocompatible polymeric materials such as a hydrogel polymer, polymethyldisiloxane, polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and mixtures thereof. The coatings may optionally be further covered by a suitable topcoat of fluorosilicone, polysaccarides, polyethylene glycol, phospholipids or combinations thereof to impart controlled release characteristics in the composition. A variety of compositions and methods related to stent coating and/or local stent drug delivery for preventing restenosis are known in the art (see, for example, U.S. Pat. Nos. 6,517,889; 6,273,913; 6,258,121; 6,251,136; 6,248,127; 6,231,600; 6,203,551; 6,153,252; 6,071,305; 5,891,507; 5,837,313 and published U.S. patent application No.: US2001/0027340, each of which is incorporated herein by reference in its entirety). For example, stents may be coated with polymer-drug conjugates by dipping the stent in polymer-drug solution or spraying the stent with such a solution. In certain embodiment, suitable materials for the implantable device include biocompatible and nontoxic materials, and may be chosen from the metals such as nickel-titanium alloys, steel, or biocompatible polymers, hydrogels, polyurethanes, polyethylenes, ethylenevinyl acetate copolymers, etc. In certain embodiments, the inventive compound is coated onto a stent for insertion into an artery or vein following balloon angioplasty.

The compounds of this invention or pharmaceutically acceptable compositions thereof may also be incorporated into compositions for coating implantable medical devices, such as prostheses, artificial valves, vascular grafts, stents and catheters. Accordingly, the present invention, in another aspect, includes a composition for coating an implantable device comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device. In still another aspect, the present invention includes an implantable device coated with a composition comprising a compound of the present invention as described generally above, and in classes and subclasses herein, and a carrier suitable for coating said implantable device.

Within other aspects of the present invention, methods are provided for expanding the lumen of a body passageway, comprising inserting a stent into the passageway, the stent having a generally tubular structure, the surface of the structure being coated with (or otherwise adapted to release) an inventive compound or composition, such that the passageway is expanded. In certain embodiments, the lumen of a body passageway is expanded in order to eliminate a biliary, gastrointestinal, esophageal, tracheal/bronchial, urethral and/or vascular obstruction.

Methods for eliminating biliary, gastrointestinal, esophageal, tracheal/bronchial, urethral and/or vascular obstructions using stents are known in the art. The skilled practitioner will know how to adapt these methods in practicing the present invention. For example, guidance can be found in U.S. Patent Application Publication No.: 2003/0004209 in paragraphs [0146]-[0155], which paragraphs are hereby incorporated herein by reference.

Another aspect of the invention relates to a method for inhibiting the growth of multidrug resistant cells in a biological sample or a patient, which method comprises administering to the patient, or contacting said biological sample with a compound of formula I or a composition comprising said compound.

Additionally, the present invention provides pharmaceutically acceptable derivatives of the inventive compounds, and methods of treating a subject using these compounds, pharmaceutical compositions thereof, or either of these in combination with one or more additional therapeutic agents.

Another aspect of the invention relates to a method of treating or lessening the severity of a disease or condition associated with a proliferation disorder in a patient, said method comprising a step of administering to said patient, a compound of formula I or a composition comprising said compound.

It will be appreciated that the compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for the treatment of cancer and/or disorders associated with cell hyperproliferation. For example, when using the inventive compounds for the treatment of cancer, the expression “effective amount” as used herein, refers to a sufficient amount of agent to inhibit cell proliferation, or refers to a sufficient amount to reduce the effects of cancer. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the diseases, the particular anticancer agent, its mode of administration, and the like.

The compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. The expression “dosage unit form” as used herein refers to a physically discrete unit of therapeutic agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts (see, for example, Goodman and Gilman's, “The Pharmacological Basis of Therapeutics”, Tenth Edition, A. Gilman, J. Hardman and L. Limbird, eds., McGraw-Hill Press, 155-173, 2001, which is incorporated herein by reference in its entirety).

Another aspect of the invention relates to a method for inhibiting histone deacetylase activity in a biological sample or a patient, which method comprises administering to the patient, or contacting said biological sample with an inventive compound or a composition comprising said compound.

Furthermore, after formulation with an appropriate pharmaceutically acceptable carrier in a desired dosage, the pharmaceutical compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, creams or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the invention may be administered at dosage levels of about 0.001 mg/kg to about 50 mg/kg, from about 0.01 mg/kg to about 25 mg/kg, or from about 0.1 mg/kg to about 10 mg/kg of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect. It will also be appreciated that dosages smaller than 0.001 mg/kg or greater than 50 mg/kg (for example 50-100 mg/kg) can be administered to a subject. In certain embodiments, compounds are administered orally or parenterally.

Treatment Kit

In other embodiments, the present invention relates to a kit for conveniently and effectively carrying out the methods in accordance with the present invention. In general, the pharmaceutical pack or kit comprises one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Such kits are especially suited for the topical delivery of the inventive compounds. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceutical products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

EQUIVALENTS

The representative examples which follow are intended to help illustrate the invention, and are not intended to, nor should they be construed to, limit the scope of the invention. Indeed, various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including the examples which follow and the references to the scientific and patent literature cited herein. It should further be appreciated that, unless otherwise indicated, the entire contents of each of the references cited herein are incorporated herein by reference to help illustrate the state of the art. The following examples contain important additional information, exemplification and guidance which can be adapted to the practice of this invention in its various embodiments and the equivalents thereof.

These and other aspects of the present invention will be further appreciated upon consideration of the following Examples, which are intended to illustrate certain particular embodiments of the invention but are not intended to limit its scope, as defined by the claims.

EXAMPLES

The compounds of this invention and their preparation can be understood further by the examples that illustrate some of the processes by which these compounds are prepared or used. It will be appreciated, however, that these examples do not limit the invention. Variations of the invention, now known or further developed, are considered to fall within the scope of the present invention as described herein and as hereinafter claimed.

General Description of Synthetic Methods

The various references cited herein provide helpful background information on preparing compounds similar to the inventive compounds described herein or relevant intermediates, as well as information on formulation, uses, and administration of such compounds which may be of interest.

Moreover, the practitioner is directed to the specific guidance and examples provided in this document relating to various exemplary compounds and intermediates thereof.

The compounds of this invention and their preparation can be understood further by the examples that illustrate some of the processes by which these compounds are prepared or used. It will be appreciated, however, that these examples do not limit the invention. Variations of the invention, now known or further developed, are considered to fall within the scope of the present invention as described herein and as hereinafter claimed.

According to the present invention, any available techniques can be used to make or prepare the inventive compounds or compositions including them. For example, a variety of a variety combinatorial techniques, parallel synthesis and/or solid phase synthetic methods such as those discussed in detail below may be used. Alternatively or additionally, the inventive compounds may be prepared using any of a variety of solution phase synthetic methods known in the art.

It will be appreciated as described below, that a variety of inventive compounds can be synthesized according to the methods described herein. The starting materials and reagents used in preparing these compounds are either available from commercial suppliers such as Aldrich Chemical Company (Milwaukee, Wis.), Bachem (Torrance, Calif.), Sigma (St. Louis, Mo.), or are prepared by methods well known to a person of ordinary skill in the art following procedures described in such references as Fieser and Fieser 1991, “Reagents for Organic Synthesis”, vols 1-17, John Wiley and Sons, New York, N.Y., 1991; Rodd 1989 “Chemistry of Carbon Compounds”, vols. 1-5 and supps, Elsevier Science Publishers, 1989; “Organic Reactions”, vols 1-40, John Wiley and Sons, New York, N.Y., 1991; March 2001, “Advanced Organic Chemistry”, 5th ed. John Wiley and Sons, New York, N.Y.; and Larock 1990, “Comprehensive Organic Transformations: A Guide to Functional Group Preparations”, 2nded. VCH Publishers. These schemes are merely illustrative of some methods by which the compounds of this invention can be synthesized, and various modifications to these schemes can be made and will be suggested to a person of ordinary skill in the art having regard to this disclosure.

The starting materials, intermediates, and compounds of this invention may be isolated and purified using conventional techniques, including filtration, distillation, crystallization, chromatography, and the like. They may be characterized using conventional methods, including physical constants and spectral data.

Synthesis of Exemplary Compounds

Unless otherwise indicated, starting materials are either commercially available or readily accessibly through laboratory synthesis by anyone reasonably familiar with the art. Described generally below, are procedures and general guidance for the synthesis of compounds as described generally and in subclasses and species herein.

Synthesis of SAHP for Use as HDAC Inhibitors

Described below is the synthesis of a SAHP, an ester-containing analog of SAHA (as shown inFIG. 12).

3.86 g (24.2 mmol) O-benzylhydroxylamine hydrochloride and 13 mL (75 mmol) diisopropylethylamine were dissolved in 100 mL methylene chloride and cooled to 0° C. 5.00 g (24.2 mmol) methyl 8-chloro-8-oxooctanoate were dissolved in 10 mL methylene chloride and slowly added to the reaction mixture. The reaction mixture was stirred for 1 h at 0° C. and warmed to room temperature. After stirring for additional 12 h, 300 mL 0.5N HCl were added. The organic layer was separated and washed with brine and sat. bicarb. After drying over sodium sulfate, the organic solvent was removed under reduced pressure and the crude product was purified on silica (methylene chloride/methanol 12:1, rf=0.7) to yield the desired compound 1 as white solid (6.3 g, 89%).

6.3 g (21.5 mmol) methyl ester 1 were dissolved in 200 mL methanol, followed by the addition of 50 mL 2N LiOH. The reaction mixture was heated to reflux for 1 h and cooled to room temperature. After addition of 100 mL 1N HCl and 200 mL water, the reaction mixture was extracted three times with 150 mL ethyl acetate. The combined organic layers were dried over sodium sulfate and the solvent was removed under reduced pressure to afford the carboxylic acid 2 pure and in quantitative yields as white solid

140 mg carboxylic acid 2 (5 mmol), 56.5 mg phenol (6 mmol) and 113 mg dicyclohexylcarbodiimide (5.5 mmol) are mixed followed by the addition of 10 mL methylene chloride and 30 mg 4-Dimethylaminopyridine. The reaction mixture was stirred for 2 h and applied crude on a silica column followed by elution with haxanes/ethyl acetate (10-100% ethyl acetate). The desired phenol ester 3 was obtained as a white solid in 87% yield (155 mg).

80 mg phenol ester 3 (0.225 mmol) are dissolved in methanol. A catalytical amount of palladium on charcoal (10%) was as added and hydrogen was bubbled through the reaction mixture. After 1 h hour no starting material was detectable by TLC. The reaction mixture was filtered through Celite and the solvent was removed under reduced pressure to yield the free hydroxamte SAHP as brownish solid in quantitative yields (59 mg). The crude product did not show any impurities as judged by LCMS and NMR.

Biological Assay Procedures

Cell Culture and Transfections.

TAg-Jurkat cells were transfected by electroporation with 5 μg of FLAG-epitope-tagged pBJ5 constructs for expression of recombinant proteins. Cells were harvested 48 h posttransfection.

[3H]Acetate-incorporated histones were isolated from butyrate-treated HeLa cells by hydroxyapatite chromatography (as described in Tong, et al.Nature1997, 395, 917-921.) Immunoprecipitates were incubated with 1.4 μg (10,000 dpm) histones for 3 h at 37° C. HDAC activity was determined by scintillation counting of the ethyl acetate-soluble [3H]acetic acid (as described in Taunton, et al.,Science1996, 272, 408-411). Compounds were added in DMSO such that final assay concentrations were 1% DMSO. IC50s were calculated using Prism 3.0 software. Curve fitting was done without constraints using the program's Sigmoidal-Dose Response parameters. All data points were acquired in duplicate and IC50s are calculated from the composite results of at least two separate experiments.

In Vivo Activity

Although a variety of methods can be utilized, one exemplary method by which the in vivo activity of the inventive compounds is determined is by subcutaneously transplanting a desired tumor mass in mice. Drug treatment is then initiated when tumor mass reaches approximately 100 mm3after transplantation of the tumor mass. A suitable composition, as described in more detail above, is then administered to the mice, preferably in saline and also preferably administered once a day at doses of 5, 10 and 25 mg/kg, although it will be appreciated that other doses can also be administered. Body weight and tumor size are then measured daily and changes in percent ratio to initial values are plotted. In cases where the transplanted tumor ulcerates, the weight loss exceeds 25-30% of control weight loss, the tumor weight reaches 10% of the body weight of the cancer-bearing mouse, or the cancer-bearing mouse is dying, the animal is sacrificed in accordance with guidelines for animal welfare.

Assays to Identify Potential Antiprotozoal Compounds by Inhibition of Histone Deacetylase

As detailed in U.S. Pat. No. 6,068,987, inhibitors of histone deacetylases may also be useful as antiprotozoal agents. Described therein are assays for histone deacetylase activity and inhibition and describe a variety of known protozoal diseases. The entire contents of U.S. Pat. No. 6,068,987 are hereby incorporated by reference.