Title of Invention

BIFUNCTIONAL HISTONE DEACETYLASE INHIBITORS

Abstract In recognition of the need to develop novel therapeutic agents and efficient methods for the synthesis thereof, the present invention provides novel bifunctional, trifunctional, or multifunctional compounds for inhibiting histone deacetylases, and pharmaceutically acceptable salts and derivatives thereof. The present invention further provides methods for treating disorders regulated by histone deacetylase activity (e.g., proliferative diseases, cancer, inflammatory diseases, protozoal infections, hair loss, etc.) comprising administering a therapeutically effective amount of an inventive compound to a subject in need thereof. The present invention also provides methods for preparing compounds of the invention.
Full Text Bifunctional Histone Deacetylase Inhibitors
Related Applications
[0001] The present invention claims priority under 35 U.S.C. § 119(e) to U.S. provisional
patent application, USSN 60/773,510, filed February 14,2006, which is incorporated herein
by reference.
Background of the Invention
[0002] The identification of small organic molecules that affect specific biological
functions is an endeavor that impacts both biology and medicine. Such molecules are useful
as therapeutic agents and as probes of biological function. In but one example from the
emerging field of chemical genetics, in which small molecules can be used to alter the
function of biological molecules to which they bind, these molecules have been useful at
elucidating signal transduction pathways by acting as chemical protein knockouts, thereby
causing a loss of protein function. (Schreiber et al, J. Am. Chem. Soc., 1990,112, 5583;
Mitchison, Chem. and Biol., 1994,1,3) Additionally, due to the interaction of these small
molecules with particular biological targets and their ability to affect specific biological
function (e.g. gene transcription), they may also serve as candidates for the development of
new therapeutics. One important class of small molecules, natural products, which are small
molecules obtained from nature, clearly have played an important role in the development of
biology and medicine, serving as pharmaceutical leads, drugs (Newman et al., Nat. Prod.
Rep. 2000,17, 215-234), and powerful reagents for studying cell biology (Schreiber, S.L.
Chem. and Eng. News 1992 (October 26), 22-32).
[0003] One biological target of recent interest is histone deacetylase (see, for example, a
discussion of the use of inhibitors of histone deacetylases for the treatment of cancer: Marks
et al. Nature Reviews Cancer 2001, 1, 194; Johnstone et al. Nature Reviews Drug Discovery
2002,1,287). Post-translational modification of proteins through acetylation and
deacetylation of lysine residues plays a critical role in regulating their cellular functions.
HDACs are zinc hydrolases that modulate gene expression through deacetylation of the N-
acetyl-lysine residues of histone proteins and other transcriptional regulators (Hassig et al.
Curr. Opin. Chem. Biol 1997, 1, 300-308). HDACs participate in cellular pathways that
control cell shape and differentiation, and an HDAC inhibitor has been shown effective in
treating an otherwise recalcitrant cancer (Warrell et al. J. Natl. Cancer Inst.. 1998, 90,1621-

1625). At this time, eleven human HDACs, which use zinc as a cofactor, have been
identified (Taunton et al. Science 1996,272,408-411; Yang et al. J. Biol. Chem. 1997, 272,
28001-28007. Grozinger et al Proc. Natl. Acad. Sci. U.SA. 1999,96,4868-4873; Kao et al.
Genes Dev. 2000,14, 55-66. Hu et al. J. Biol Chem. 2000,275,15254-15264; Zhou et al.
Proc. Natl. Acad. Sci. U.SA. 2001,98,10572-10577; Venter etal Science 2001,291, 1304-
1351) these members fall into three classes (class I, II, and III). An additional seven HDACs
have been identified which use NAD as a confactor. To date, no small molecules are known
that selectively target either the two classes or individual members of this family ((for
example ortholog-selective HDAC inhibitors have been reported: Meinke et al. J. Med.
Chem. 2000,14, 4919-4922; Meinke, etal. Curr. Med. Chem. 2001, 8, 211-235).
Summary of the Invention
[0004J The present invention provides novel bifunctional or multifunctional histone
deacetylase inhibitors and methods of preparing and using these compounds. These
compounds are particularly useful in the treatment of proliferative disease such as cancer.
Certain compounds may be particularly useful in specifically inhibiting one class or member
of HDACs. Certain compounds may be particularly useful in specifically inhibiting other
deacetylation enzymes such as tubulin deacetylase (TDAC).
[0005] The present invention provides novel inhibitors of HDACs based on the
observation that histone deacetylases form dimeric units in some cases and that some HDACs
have two catalytic domains (e.g., HDAC6 has two functionally active HDAC domains, and
HDAC10 has one functionally active HDAC domain and one truncated inactive HDAC
domain). Histone deacetylases form both homodimers and heterodimers. Therefore, the
compounds of the invention are generally two functional groups known to inhibit histone
deacetylase (eg., zinc chelating moieties) linked together covalently via a tinker moiety. The
compounds of the invention may also include more than two functional groups known to
inhibit HDACs. Trimeric, multimeric, and polymeric compounds are considered part of the
invention. In certain embodiments, the inhibitory functional groups are known to bind the
Zn+2 ion found in the catalytic site of HDACs. Exemplary functional groups known to inhibit
HDACs include:


When the inventive compound is bifunctional, the inventive compound may be two of the
same inhibitory functional groups linked together, or it may comprises two different
functional groups linked together. So too with trimeric, multimeric, or polymeric
compounds, the compound may comprises the same inhibitory functional groups or different
inhibitory functional groups. Certain preferred inhibitory functional groups include
hydroxamic acids, cinnamic hydroxamic acids, thiols, carboxlic acids, and ortho-
aminoanilides. In certain embodiments, at least one of the inhibitory functional groups is
hydroxamic acid. In other embodiments, at least one of the inhibitory functional groups is an
ortho-aminoanilide. In yet other embodiments, at least one of the inhibitory functional
groups is a thiol-containing functional group. Pro-drug or protected forms of these functional
groups (e.g., esters) may also be used in the inventive compounds.
[0006] The present invention provides novel compounds of the general formula (I),
wherein
A comprises a functional group that inhibits histone deacetylase;
B comprises a functional group that inhibits histone deacetylase, wherein A and B
may be the same or different; and
L is a linker covalently binding together A and B; and
and pharmaceutical compositions thereof. The compounds of the invention are described
generally and in subclasses herein. These compounds are useful particularly as inhibitors of

HDACs, and thus are useful for the treatment of proliferative diseases (e.g., cancer, benign
neoplasms, diabetic retinopathy, inflammatory diseases, angiogenesis, infectious diseases).
The compounds may also be useful in treating skin disorders such as hair loss and skin
hyperpigmentation. The inventive compounds are additionally useful as tools to probe
biological function (e.g., the dimerization of histone deacetylases).
[0007] In another aspect, the present invention provides methods for inhibiting histone
deacetylase activity in a patient or a biological sample, comprising administering to the
patient, or contacting the biological sample with an effective inhibitory amount of an
inventive compound. In still another aspect, the present invention provides methods for
treating skin disorders involving histone deacetylase activity, comprising administering
topically to a subject in need thereof a therapeutically effective amount of a compound of the
invention, wherein the compound includes an esterase-senstive bond (e.g., an ester bond).
The invention also provides kits for using the inventive compounds in the clinic or in a
research setting.
[0008] In yet another aspect, the present invention provides methods for preparing
compounds of the invention and intermediates thereof.
Definitions
[0009] Certain compounds of the present invention, and definitions of specific functional
groups are also described in more detail below. For purposes of this invention, the chemical
elements are identified in accordance with the Periodic Table of the Elements, CAS version,
Handbook of Chemistry and Physics, 75* Ed., inside cover, and specific functional groups
are generally defined as described therein. Additionally, general principles of organic
chemistry, as well as specific functional moieties and reactivity, are described in "Organic
Chemistry", Thomas Sorrell, University Science Books, Sausalito: 1999, the entire contents
of which are incorporated herein by reference. Furthermore, it will be appreciated by one of
ordinary skill in the art that the synthetic methods, as described herein, utilize a variety of
protecting groups.
[0010] It will be appreciated that the compounds, as described herein, may be substituted
with any number of substituents or functional moieties. In general, the term "substituted"
whether preceded by the term "optionally" or not, and substituents contained in formulas of
this invention, refer to the replacement of hydrogen radicals in a given structure with the
radical of a specified substituent When more than one position in any given structure may
be substituted with more than one substituent selected from a specified group, the substituent

may be either the same or different at every position. As used herein, the term "substituted"
is contemplated to include all permissible substituents of organic compounds. In a broad
aspect, the permissible substituents include acyclic and cyclic, branched and unbranched,
carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds.
For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents
and/or any permissible substituents of organic compounds described herein which satisfy the
valencies of the heteroatoms. Furthermore, this invention is not intended to be limited in any
manner by the permissible substituents of organic compounds. Combinations of substituents
and variables envisioned by this invention are preferably those that result in the formation of
stable compounds useful in the treatment, for example of proliferative disorders, including,
but not limited to cancer. The term "stable", as used herein, preferably refers to compounds
which possess stability sufficient to allow manufacture and which maintain the integrity of
the compound for a sufficient period of time to be detected and preferably for a sufficient
period of time to be useful for the purposes detailed herein.
[0011] The term "acyl", as used herein, refers to a carbonyl-containing functionality, e.g.,
-C(=O)R, wherein R is an aliphatic, alycyclic, heteroaliphatic, heterocyclic, aryl, heteroaryl,
(aliphatic)aryl, (heteroaliphatic)aryl, heteroaliphatic(aryl) or heteroaliphatic(heteroaryl)
moiety, whereby each of the aliphatic, heteroaliphatic, aryl, or heteroaryl moieties is
substituted or unsubstituted, or is a substituted (e.g., hydrogen or aliphatic, heteroaliphatic,
aryl, or heteroaryl moieties) oxygen or nitrogen containing functionality (e.g., forming a
carboxylic acid, ester, or amide functionality).
[0012] The term "aliphatic", as used herein, includes both saturated and unsaturated,
straight chain (i.e., unbranched) or branched aliphatic hydrocarbons, which are optionally
substituted with one or more functional groups. As will be appreciated by one of ordinary
skill in the art, "aliphatic" is intended herein to include, but is not limited to, alkyl, alkenyl,
alkynyl moieties. Thus, as used herein, the term "alkyl" includes straight and branched alkyl
groups. An analogous convention applies to other generic terms such as "alkenyl", "alkynyl"
and the like. Furthermore, as used herein, the terms "alkyl", "alkenyl", "alkynyl" and the like
encompass both substituted and unsubstituted groups. In certain embodiments, as used
herein, "lower alkyl" is used to indicate those alkyl groups (substituted, unsubstituted,
branched or unbranched) having 1-6 carbon atoms.
[0013] In certain embodiments, the alkyl, alkenyl and alkynyl groups employed in the
invention contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl,
alkenyl, and alkynyl groups employed in the invention contain 1-10 aliphatic carbon atoms.

In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention
contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and
alkynyl groups employed in the invention contain 1-6 aliphatic carbon atoms. In yet other
embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-4
carbon atoms. Illustrative aliphatic groups thus include, but are not limited to, for example,
methyl, ethyl, n-propyl, isopropyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, n-pentyl, sec-
pentyl, isopentyl, tert-pentyl, n-hexyl, sec-hexyl, moieties and the like, which again, may bear
one or more substituents. Alkenyl groups include, but are not limited to, for example,
ethenyl, propenyl, butenyl, l-methyl-2-buten-l-yl, and the like. Representative alkynyl
groups include, but are not limited to, ethynyl, 2-propynyl (propargyl), 1-propynyl and the
like.
[0014] The term "alicyclic", as used herein, refers to compounds which combine the
properties of aliphatic and cyclic compounds and include but are not limited to cyclic, or
polycyclic aliphatic hydrocarbons and bridged cycloalkyl compounds, which are optionally
substituted with one or more functional groups. As will be appreciated by one of ordinary
skill in the art, "alicyclic" is intended herein to include, but is not limited to, cycloalkyl,
cycloalkenyl, and cycloalkynyl moieties, which are optionally substituted with one or more
functional groups. Illustrative alicyclic groups thus include, but are not limited to, for
example, cyclopropyl, -CH2-cyclopropyl, cyclobutyl, -CH2-cyclobutyl, cyclopentyl, -CH2-
cyclopentyl-n, cyclohexyl, -CH2-cyclohexyl, cyclohexenylethyl, cyclohexanylethyl,
norborbyl moieties and the like, which again, may bear one or more substituents.
[0015] The term "alkoxy" (or “alkyloxy"), or "thioalkyl" as used herein refers to an alkyl
group, as previously defined, attached to the parent molecular moiety through an oxygen
atom or through a sulfur atom. In certain embodiments, the alkyl group contains 1-20
aliphatic carbon atoms. In certain other embodiments, the alkyl group contains 1-10 aliphatic
carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in
the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl group
contains 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl group contains 1-4
aliphatic carbon atoms. Examples of alkoxy, include but are not limited to, methoxy, ethoxy,
propoxy, isopropoxy, n-butoxy, tert-butoxy, neopentoxy and n-hexoxy. Examples of
thioalkyl include, but are not limited to, methylthio, ethylthio, propylthio, isopropylthio, n-
butylthio, and the like.
[0016] The term "alkylamino" refers to a group having the structure -NHR'wherein R' is
alkyl, as defined herein. The term "aminoalkyl" refers to a group having the structure

NH2R'-, wherein R' is alkyl, as defined herein. In certain embodiments, the alkyl group
contains 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl group contains
1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl
groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other
embodiments, the alkyl group contains 1-6 aliphatic carbon atoms. In yet other
embodiments, the alkyl group contains 1-4 aliphatic carbon atoms. Examples of alkylamino
include, but are not limited to, methylamino, ethylamino, iso-propylamino and the like.
[0017] Some examples of substituents of the above-described aliphatic (and other)
moieties of compounds of the invention include, but are not limited to aliphatic;
heteroaliphatic; aryl; heteroaryl; alkylaryl; alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy;
heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br, I; -OH; -NO2; -
CN; -CF3; -CH2CF3; -CHCI2; -CH2OH; -CH2CH2OH; -CH2NH2; -CH2SO2CH3; -C(O)Rx; -
CO2(Rx); -CON(Rx)2; -OC(O)Rx; -OCO2Rx; -OCON(Rx)2; -N(Rx)2; -S(O)2Rx; -NRx(CO)Rx
wherein each occurrence of Rx independently includes, but is not limited to, aliphatic,
alycyclic, heteroaliphatic, heterocyclic, aryl, heteroaryl, alkylaryl, or alkylheteroaryl, wherein
any of the aliphatic, heteroaliphatic, alkylaryl, or alkylheteroaryl substituents described above
and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic,
and wherein any of the aryl or heteroaryl substituents described above and herein may be
substituted or unsubstituted. Additional examples of generally applicable substituents are
illustrated by the specific embodiments shown in the Examples that are described herein.
[0018} In general, the term "aryl", as used herein, refers to a stable mono- or polycyclic,
unsaturated moiety having preferably 3-14 carbon atoms, each of which may be substituted or
unsubstituted. In certain embodiments, the term "aryl" refers to a planar ring having p-
orbitals perpendicular to the plane of the ring at each ring atom and satisfying the Huckel rule
where the number of pi electrons in the ring is (4n+2) wherein n is an integer. A mono- or
polycyclic, unsaturated moiety that does not satisfy one or all of these criteria for aromaticity
is defined herein as "non-aromatic", and is encompassed by the term "alicyclic".
[0019] In general, the term "heteroaryl", as used herein, refers to a stable mono- or
polycyclic, unsaturated moiety having preferably 3-14 carbon atoms, each of which may be
substituted or unsubstituted; and comprising at least one heteroatom selected from O, S, and
N within the ring (i.e., in place of a ring carbon atom). In certain embodiments, the term
"heteroaryl" refers to a planar ring comprising at least on eheteroatom, having p-orbitals
perpendicular to the plane of the ring at each ring atom, and satisfying the Huckel rule where
the number of pi electrons in the ring is (4n+2) wherein n is an integer.

[0020] It will also be appreciated that aryl and heteroaryl moieties, as defined herein may
be attached via an alkyl or heteroalkyl moiety and thus also include -(alkyl)aryl, -
(heteroalkyl)aryl, -(heteroalkyl)heteroaryl, and (heteroalkyl)heteroaryl moieties. Thus, as
used herein, the phrases "aryl or heteroaryl moieties" and "aryl, heteroaryl, (alkyl)aryl, -
(heteroalkyl)aryl, -(heteroalkyl)heteroaryl, and (heteroalkyl)heteroaryl" are interchangeable.
Substituents include, but are not limited to, any of the previously mentioned substituents, i.e.,
the substituents recited for aliphatic moieties, or for other moieties as disclosed herein,
resulting in the formation of a stable compound.
[00211 The term "aryl", as used herein, does not differ significantly from the common
meaning of the term in the art, and refers to an unsaturated cyclic moiety comprising at least
one aromatic ring. In certain embodiments, "aryl" refers to a. mono- or bicyclic carbocyclic
ring system having one or two aromatic rings including, but not limited to, phenyl, naphthyl,
tetrahydronaphthyl, indanyl, indenyl and the like.
[0022] The term "heteroaryl", as used herein, does not differ significantly from the
common meaning of the term in the art, and refers to a cyclic aromatic radical having from
five to ten ring atoms of which one ring atom is selected from S, O and N; zero, one or two
ring atoms are additional heteroatoms independently selected from S, O and N; and the
remaining ring atoms are carbon, the radical being joined to the rest of the molecule via any
of the ring atoms, such as, for example, pyridyl, pyrazinyl, pyrirnidinyl, pyrrolyl, pyrazolyl,
imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl,
quinolinyl, isoquinolinyl, and the like.
[0023] It will be appreciated that aryl and heteroaryl groups (including bicyclic aryl
groups) can be unsubstituted or substituted, wherein substitution includes replacement of one
or more of the hydrogen atoms thereon independently with any one or more of the following
moieties including, but not limited to: aliphatic; alicyclic; heteroaliphatic; heterocyclic;
aromatic; heteroaromatic; aryl; heteroaryl; alkylaryl; heteroalkylaryl; alkylheteroaryl;
heteroalkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio;
heteroalkylthio; heteroarylthio; F; C1; Br; I; -OH; -NO2; -CN; -CF3; -CH2CF3; -CHC12; -
CH2OH; -CH2CH2OH; -CH2NH2; -CH2SO2CH3; -C(O)Rx; -CO2(Rx); -CON(Rx)2; -OC(O)Rx;
-OCO2Rx; -OCON(Rx)2; -N(Rx)2; -S(O)Rx; -S(O)2Rx; -NRx(CO)Rx wherein each occurrence
of Rx independently includes, but is not limited to, aliphatic, alicyclic, heteroaliphatic,
heterocyclic, aromatic, heteroaromatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl,
heteroalkylaryl or heteroalkylheteroaryl, wherein any of the aliphatic, alicyclic,
heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroaryl substituents described above and

herein may be substituted or unsubstituted, branched or unbranched, saturated or unsaturated,
and wherein any of the aromatic, heteroaromatic, aryl, heteroaryl, -(alkyl)aryl or -
(alkyl)heteroaryl substituents described above and herein may be substituted or unsubstituted.
Additionally, it will be appreciated, that any two adjacent groups taken together may
represent a 4, 5,6, or 7-membered substituted or unsubstituted alicyclic or heterocyclic
moiety. Additional examples of generally applicable substituents are illustrated by the
specific embodiments described herein.
[0024] The term "cycloalkyl", as used herein, refers specifically to groups having three to
seven, preferably three to ten carbon atoms. Suitable cycloalkyls include, but are not limited
to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and the like, which, as in the
case of aliphatic, alicyclic, heteroaliphatic or heterocyclic moieties, may optionally be
substituted with substituents including, but not limited to aliphatic; alicyclic; heteroaliphatic;
heterocyclic; aromatic; heteroaromatic; aryl; heteroaryl; alkylaryl; heteroalkylaryl;
alkylheteroaryl; heteroalkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy;
alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br, I; -OH; -NO2; -CN; -CF3; -
CH2CF3; -CHC12; -CH2OH; -CH2CH2OH; -CH2NH2; -CH2SO2CH3; -C(O)Rx; -CO2(Rx); -
CON(Rx)2; -OC(O)Rx; -OCO2Rx; -OCON(Rx)2; -N(Rx)2; -S(O)2Rx; -NRx(CO)Rx wherein
each occurrence of Rx independently includes, but is not limited to, aliphatic, alicyclic,
heteroaliphatic, heterocyclic, aromatic, heteroaromatic, aryl, heteroaryl, alkylaryl,
alkylheteroaryl, heteroalkylaryl or heteroalkylheteroaryl, wherein any of the aliphatic,
alicyclic, heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroaryl substituents described
above and herein may be substituted or unsubstituted, branched or unbranched, saturated or
usaturated, and wherein any of the aromatic, heteroaromatic, aryl or heteroaryl substituents
described above and herein may be substituted or unsubstituted. Additional examples of
generally applicable substituents are illustrated by the specific embodiments shown in the
Examples that are described herein.
[0025] The term "heteroaliphatic", as used herein, refers to aliphatic moieties in which
one or more carbon atoms in the main chain have been substituted wiih a heteroatom. Thus,
a heteroaliphatic group refers to an aliphatic chain which contains one or more oxygen,
sulfur, nitrogen, phosphorus or silicon atoms, e.g., in place of carbon atoms. Heteroaliphatic
moieties may be linear or branched, and saturated 0 runsaturated. In certain embodiments,
heteroaliphatic moieties are substituted by independent replacement of one or more of the
hydrogen atoms thereon with one or more moieties including, but not limited to aliphatic;
alicyclic; heteroaliphatic; heterocyclic; aromatic; heteroaromatic; aryl; heteroaryl; alkylaryl;

alkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio;
heteroalkylthio; heteroarylthio; F; Cl; Br; I; -OH; -NO2; -CN; -CF3; -CH2CF3; -CHC12; -
CH2OH; -CH2CH2OH; -CH2NH2; -CH2SO2CH3- -C(O)Rx; -CO2(Rx); -CON(Rx)2; -OC(O)Rx;
-OCO2Rx; -OCON(Rx)2; -N(Rx)2; -S(O)2Rx; -NRx(CO)Rx wherein each occurrence of Rx
independently includes, but is not limited to, aliphatic, alicyclic, heteroaliphatic, heterocyclic,
aromatic, heteroaromatic, aryl, heteroaryl, alkylaryl, alkylheteroaryl, heteroalkylaryl or
heteroalkylheteroaryl, wherein any of the aliphatic, alicyclic, heteroaliphatic, heterocyclic,
alkylaryl, or alkylheteroaryl substituents described above and herein may be substituted or
unsubstituted, branched or unbranched, saturated or unsaturated, and wherein any of the
aromatic, heteroaromatic, aryl or heteroaryl substituents described above and herein may be
substituted or unsubstituted. Additional examples of generally applicable substituents are
illustrated by the specific embodiments described herein.
[0026] The term "heterocycloalkyl", "heterocycle" or "heterocyclic", as used herein,
refers to compounds which combine the properties of heteroaliphatic and cyclic compounds
and include, but are not limited to, saturated and unsaturated mono- or polycyclic cyclic ring
systems having 5-16 atoms wherein at least one ring atom is a heteroatom selected from 0, S
and N (wherein the nitrogen and sulfur heteroatoms may be optionally be oxidized), wherein
the ring systems are optionally substituted with one or more functional groups, as defined
herein. In certain embodiments, the term "heterocycloalkyl", "heterocycle" or "heterocyclic"
refers to a non-aromatic 5-, 6- or 7- membered ring or a polycyclic group wherein at least one
ring atom is a heteroatom selected from O, S, and N (wherein the nitrogen and sulfur
heteroatoms may be optionally be oxidized), including, but not limited to, a bi- or tri-cyclic
group, comprising fused six-membered rings having between one and three heteroatoms
independently selected from oxygen, sulfur and nitrogen, wherein (i) each 5-membered ring
has 0 to 2 double bonds, each 6-membered ring has 0 to 2 double bonds and each 7-
membered ring has 0 to 3 double bonds, (ii) the nitrogen and sulfur heteroatoms may be
optionally be oxidized, (iii) the nitrogen heteroatom may optionally be quaternized, and (iv)
any of the above heterocyclic rings may be fused to an aryl or heteroaryl ring. Representative
heterocycles include, but are not limited to, heterocycles such as furanyl, thiofuranyl,
pyranyl, pyrrolyl, thienyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl,
imidazolidinyl, piperidinyl, piperazinyl, oxazolyl, oxazolidinyl, isooxazolyl, isoxazolidinyl,
dioxazolyl, thiadiazolyl, oxadiazolyl, tetrazolyl, triazolyl, thiatriazolyl, oxatriazolyl,
thiadiazolyl, oxadiazolyl, morpholinyl, thiazolyl, thiazolidinyl, isothiazolyl, isothiazolidinyl,
dithiazolyl, dithiazolidinyl, tetrahydrofuryl, and benzofused derivatives thereof. In certain

embodiments, a "substituted heterocycle, or heterocycloalkyl or heterocyclic" group is
utilized and as used herein, refers to a heterocycle, or heterocycloalkyl or heterocyclic group,
as defined above, substituted by the independent replacement of one, two or three of the
hydrogen atoms thereon with, but are not limited to, aliphatic; alicyclic; heteroaliphatic;
heterocyclic; aromatic; heteroaromatic; aryl; heteroaryl; alkylaryl; heteroalkylaryl;
alkylheteroaryl; heteroalkylheteroaryl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy;
alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; - OH; -NO2; -CN; -CF3; -
CH2CF3; -CHC12; -CH2OH; -CH2CH2OH; -CH2NH2; -CH2SO2CH3; -C(O)Rx; -CO2(Rx); -
CON(Rx)2; -OC(O)Rx; -OCO2Rx; -OCON(Rx)2; -N(Rx)2; -S(O)2Rx; -NRx(CO)Rx wherein
each occurrence of Rx independently includes, but is not limited to, aliphatic, alicyclic,
heteroaliphatic, heterocyclic, aromatic, heteroaromatic, aryl, heteroaryl, alkylaryl,
alkylheteroaryl, heteroalkylaryl or heteroalkylheteroaryl, wherein any of the aliphatic,
alicyclic, heteroaliphatic, heterocyclic, alkylaryl, or alkylheteroaryl substituents described
above and herein may be substituted or unsubstituted, branched or unbranched, saturated or
unsaturated, and wherein any of the aromatic, heteroaromatic, aryl or heteroaryl substitutents
described above and herein may be substituted or unsubstituted. Additional examples or
generally applicable substituents are illustrated by the specific embodiments described herein.
[0027] Additionally, it will be appreciated that any of the alicyclic or heterocyclic
moieties described above and herein may comprise an aryl or heteroaryl moiety fused thereto.
Additional examples of generally applicable substituents are illustrated by the specific
embodiments described herein. The terms "halo" and "halogen" as used herein refer to an
atom selected from fluorine, chlorine, bromine, and iodine.
[0028] The terms "halo" and "halogen" as used herein refer to an atom selected from
fluorine, chlorine, bromine, and iodine.
[0029] The term "haloalkyl" denotes an alkyl group, as defined above, having one, two,
or three halogen atoms attached thereto and is exemplified by such groups as chloromethyl,
bromoethyl, trifluoromethyl, and the like.
[0030] The term "amino", as used herein, refers to a primary (-NH2), secondary (-NHRx),
tertiary (-NRxRy), or quaternary (-N+RxRyRz) amine, where Rx, Ry and Rz are independently
an aliphatic, alicyclic, heteroaliphatic, heterocyclic, aryl, or heteroaryl moiety, as defined
herein. Examples of amino groups include, but are not limited to, methylamino,
dimethylamino, ethylamino, diethylamino, diethylaminocarbonyl, methylethylamino, iso-
propylamino, piperidino, trimethylamino, and propylamino.

[0031] The term "alkylidene", as used herein, refers to a substituted or unsubstituted,
linear or branched saturated divalent radical consisting solely of carbon and hydrogen atoms,
having from one to n carbon atoms, having a free valence "-" at both ends of the radical. In
certain embodiments, the alkylidene moiety has 1 to 6 carbon atoms.
[0032] The term "alkenylidene", as used herein, refers to a substituted or unsubstituted,
linear or branched unsaturated divalent radical consisting solely of carbon and hydrogen
atoms, having from two to n carbon atoms, having a free valence "-" at both ends of the
radical, and wherein the unsaturation is present only as double bonds and wherein a double
bond can exist between the first carbon of the chain and the rest of the molecule. In certain
embodiments, the alkenylidene moiety has 2 to 6 carbon atoms.
[0033] The term "alkynylidene", as used herein, refers to a substituted or unsubstituted,
linear or branched unsaturated divalent radical consisting solely of carbon and hydrogen
atoms, having from two to n carbon atoms, having a free valence "-" at both ends of the
radical, and wherein the unsaturation is present only as triple or doulbe bonds and wherein a
triple or double bond can exist between the first carbon of the chain and the rest of the
molecule. In certain embodiments, the alkynylidene moiety has 2 to 6 carbon atoms.
[0034] Unless otherwise indicated, as used herein, the terms "alkyl", "alkenyl",
"alkynyl", "heteroalkyl", "heteroalkenyl", "heteroalkynyl", "alkylidene", alkenylidene", -
(alkyl)aryl, -(heteroalkyl)aryl, -(heteroalkyl)aryl, -(heteroalkyl)heteroaryl, and the like
encompass substituted and unsubstituted, and linear and branched groups. Similarly, the
terms "aliphatic", "heteroaliphatic", and the like encompass substituted and unsubstituted,
saturated and unsaturated, and linear and branched groups. Similarly, the terms "cycloalkyl",
"heterocycle", "heterocyclic", and the like encompass substituted and unsubstituted, and
saturated and unsaturated groups. Additionally, the terms "cycloalkenyl", "cycloalkynyl",
"heterocycloalkenyl", "heterocycloalkynyl", "aromatic", "heteroaromatic, "aryl",
"heteroaryl" and the like encompass both substituted and unsubstituted groups.
[0035] The phrase, "pharmaceutically acceptable derivative", as used herein, denotes any
pharmaceutically acceptable salt, ester, or salt of such ester, of such compound, or any other
adduct or derivative which, upon administration to a patient, is capable of providing (directly
or indirectly) a compound as otherwise described herein, or a metabolite or residue thereof.
Pharmaceutically acceptable derivatives thus include among others pro-drugs. A pro-drug is
a derivative of a compound, usually with significantly reduced pharmacological activity,
which contains an additional moiety, which is susceptible to removal in vivo yielding the
parent molecule as the pharmacologically active species. An example of a pro-drug is an

ester, which is cleaved in vivo to yield a compound of interest. Pro-drugs of a variety of
compounds, and materials and methods for derivatizing the parent compounds to create the
pro-drugs, are known and may be adapted to the present invention. Pharmaceutically
acceptable derivatives also include "reverse pro-drugs." Reverse pro-drugs, rather than being
activated, are inactivated upon absorption. For example, as discussed herein., many of the
ester-containing compounds of the invention are biologically active but are inactivated upon
exposure to certain physiological environments such as a blood, lymph, serum, extracellular
fluid, etc. which contain esterase activity. The biological activity of reverse pro-drags and
pro-drugs may also be altered by appending a functionality onto the compound, which may
be catalyzed by an enzyme. Also, included are oxidation and reduction reactions, including
enzyme-catalyzed oxidation and reduction reactions. Certain exemplary pharmaceutical
compositions and pharmaceutically acceptable derivatives will be discussed in more detail
herein below.
[0036] By the term "protecting group", has used herein, it is meant that a particular
functional moiety, e.g., O, S, or N, is temporarily blocked so that a reaction can be carried out
selectively at another reactive site in a multifunctional compound. In preferred embodiments,
a protecting group reacts selectively in good yield to give a protected substrate that is stable
to the projected reactions; the protecting group must be selectively removed in good yield by
readily available, preferably nontoxic reagents that do not attack the other functional groups;
the protecting group forms an easily separable derivative (more preferably without the
generation of new stereogenic centers); and the protecting group has a minimum of additional
functionality to avoid further sites of reaction. As detailed herein, oxygen, sulfur, nitrogen
and carbon protecting groups may be utilized. For example, in certain embodiments, as
detailed herein, certain exemplary oxygen protecting groups are utilized. These oxygen
protecting groups include, but are not limited to methyl ethers, substituted methyl ethers (e.g.,
MOM (methoxymethyl ether), MTM (methylthiomethyl ether), BOM (benzyloxymethyl
ether), PMBM or MPM (p-methoxybenzyloxymethyl ether), to name a few), substituted ethyl
ethers, substituted benzyl ethers, silyl ethers (e.g., TMS (trimethylsilyl ether), TES
(triethylsilylether), TIPS (triisopropylsilyl ether), TBDMS (t-butyldimethylsilyl ether),
tribenzyl silyl ether, TBDPS (t-butyldiphenyl silyl ether), to name a few), esters (e.g.,
formate, acetate, benzoate (Bz), trifluoroacetate, dichloroacetate, to name a few), carbonates,
cyclic acetals and ketals. In certain other exemplary embodiments, nitrogen protecting
groups are utilized. These nitrogen protecting groups include, but are not limited to,
carbamates (including methyl, ethyl and substituted ethyl carbamates (e.g., Troc), to name a

few) amides, cyclic imide derivatives, N-Alkyl and N-Aryl amines, imine derivatives, and
enamine derivatives, to name a few. Certain other exemplary protecting groups are detailed
herein, however, it will be appreciated that the present invention is not intended to be limited
to these protecting groups; rather, a variety of additional equivalent protecting groups can be
readily identified using the above criteria and utilized in the present invention. Additionally,
a variety of protecting groups are described in Protective Groups in Organic Synthesis, Third
Ed. Greene, T.W. and Wuts, P.G., Eds., John Wiley & Sons, New York 1999, the entire
contents of which are hereby incorporated by reference.
[0037] The term "solid support", as used herein, refers to a material having a rigid or
semi-rigid surface. Such materials will preferably take the form of small beads, pellets, disks,
chips, dishes, multi-well plates, glass slides, wafers, or the like, although other forms may be
used. In some embodiments, at least one surface of the substrate will be substantially fiat
The term "surface" refers to any generally two-dimensional structure on a solid substrate and
may have steps, ridges, kinks,, terraces, and the like without ceasing to be a surface.
[0038] The term "linker," as used herein, refers to a chemical moiety utilized to attach a
functional group (e.g., an HDAC inhibitor functional group) to another functional group to
prepare the inventive compounds. Exemplary linkers are described herein. It will be
appreciated that other linkers that are known in the art can also be employed for the synthesis
of the compounds of the invention.
[0039] "Compound": The term "compound" or "chemical compound" as used herein can
include organometallic compounds, organic compounds, metals, transitional metal
complexes, and small molecules. In certain preferred embodiments, polynucleotides are
excluded from the definition of compounds. In other preferred embodiments,
polynucleotides and peptides are excluded from the definition of compounds. In a
particularly preferred embodiment, the term compounds refers to small molecules (e.g.,
preferably, non-peptidic and non-oligomeric) and excludes peptides, polynucleotides,
transition metal complexes, metals, and organometallic compounds.
[0040] "Small Molecule": As used herein, the term "small molecule" refers to a non-
peptidic, non-oligomeric organic compound either synthesized in the laboratory or found in
nature. Small molecules, as used herein, can refer to compounds that are "natural product-
like", however, the term "small molecule" is not limited to "natural product-like"
compounds. Rather, a small molecule is typically characterized in that it contains several
carbon-carbon bonds, and has a molecular weight of less than 2000 g/mol, preferably less
than 1500 g/mol, although this characterization is not intended to be limiting for the purposes

of the present invention. Small molecules are typically characterized by multiple carbon-
carbon bonds and may have one or more stereocenters. Examples of "small molecules" that
occur in nature include, but are not limited to, taxol, dynemicin, and rapamycin. Examples of
"small molecules" that are synthesized in the laboratory include, but are not limited to,
compounds described by Tan et al ("Stereoselective Synthesis of over Two Million
Compounds Having Structural Features Both Reminiscent of Natural Products and
Compatible with Miniaturized Cell-Based Assays" J. Am. Chem. Soc. 120:8565, 1998;
incorporated herein by reference). In certain other preferred embodiments, natural-product-
like small molecules are utilized. In certain embodiments, the small molecule is not
polymeric or oligomeric. In certain embnodiments, the small molecule is not a nucleic acid,
protein, or peptide.
[0041] "Natural Product-Like Compound": As used herein, the term "natural product-
like compound" refers to compounds that are similar to complex natural products which
nature has selected through evolution. Typically, these compounds contain one or more
stereocenters, a high density and diversity of functionality, and a diverse selection of atoms
within one structure. In this context, diversity of functionality can be defined as varying the
topology, charge, size, hydrophilicity, hydrophobicity, and reactivity to name a few, of the
functional groups present in the compounds. The term, "high density of functionality", as
used herein, can preferably be used to define any molecule that contains preferably three or
more latent or active diversifiable functional moieties. These structural characteristics may
additionally render the inventive compounds functionally reminiscent of complex natural
products, in that they may interact specifically with a particular biological receptor, and thus
may also be functionally natural product-like.
[0042] "Metal chelator": As used herein, the term "metal chelator" refers to any
molecule or moiety mat is is capable of forming a complex (i.e., "chelates") with a metal ion.
In certain exemplary embodiments, a metal chelator refers to to any molecule or moiety that
"binds" to a metal ion, in solution, making it unavailable for use in chemical/enzymatic
reactions. In certain embodiments, the solution comprises aqueous environments under
physiological conditions. Examples of metal ions include, but are not limited to, Ca2+, Fe3+,
Zn2+, Na+, etc. In certain embodiments, the metal chelator bind Zn2+, which is found at the
active site of HDACs. In certain embodiments, molecules of moieties that precipitate metal
ions are not considered to be metal chelators.
[0043] As used herein the term "biological sample" includes, without limitation, cell
cultures or extracts thereof; biopsied material obtained from an animal (e.g., mammal) or

extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts
thereof. For example, the term "biological sample" refers to any solid or fluid sample
obtained from, excreted by or secreted by any living organism., including single-celled micro
organisms (such as bacteria and yeasts) and multicellular organisms (such as plants and
animals, for instance a vertebrate or a mammal, and in particular a healthy or apparently
healthy human subject or a human patient affected by a condition or disease to be diagnosed
or investigated). The biological sample can be in any form, including a solid material such as
a tissue, cells, a cell pellet, a cell extract, cell homogenates, or cell fractions; or a biopsy, or a
biological fluid. The biological fluid may be obtained from any site (e.g. blood, saliva (or a
mouth wash containing buccal cells), tears, plasma, serum, urine, bile, cerebrospinal fluid,
amniotic fluid, peritoneal fluid, and pleural fluid, or cells therefrom, aqueous or vitreous
humor, or any bodily secretion), atransudate, an exudate (e.g. fluid obtained from an abscess
or any other site of infection or inflammation), or fluid obtained from a joint (e.g. a normal
joint or a joint affected by disease such as rheumatoid arthritis, osteoarthritis, gout or septic
arthritis). The biological sample can be obtained from any organ or tissue (including a biopsy
or autopsy specimen) or may comprise cells (whether primary cells or cultured cells) or
medium conditioned by any cell, tissue or organ. Biological samples may also include
sections of tissues such as frozen sections taken for histological purposes. Biological samples
also include mixtures of biological molecules including proteins, lipids, carbohydrates and
nucleic acids generated by partial or complete fractionation of cell or tissue homogenates.
Although the sample is preferably taken from a human subject, biological samples may be
from any animal, plant, bacteria, virus, yeast, etc. The term animal, as used herein, refers to
humans as well as non-human animals, at any stage of development, including, for example,
mammals, birds, reptiles, amphibians, fish, worms and single cells. Cell cultures and live
tissue samples are considered to be pluralities of animals. In certain exemplary embodiments,
the non-human animal is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog,
a cat, a sheep, cattle, a primate, or a pig). An animal may be a transgenic animal or a human
clone. If desired, the biological sample may be subjected to preliminary processing,
including preliminary separation techniques.
Brief Description of the Drawing
[0044] Figure 1 shows exemplary tubacin-based bis-hydroxamic acids.
[0045] Figure 2 shows other exemplary bis-hydroxyamic acids, bis-cinnamic
hydroxamates.

[0046] Figure 3 shows exemplary SAHA-based bis-hydroxamic acids. Included in the
exemplary compounds are SAHA-based bis-hydroxamic acids with a linker containing an
ester bond. Such a ester-containing linker may be susceptible esterase cleavage in vivo.
[0047] Figure 4 shows exemplary bis-hydroxamates with acyl hydrazones and aryl
moieties in the linker moiety.
[0048] Figure 5 shows exemplary bis-orthoanilides with acyl hydrazones in the linker
moiety.
[0049] Figure 6 shows other exemplary homodimeric and heterodimeric HDAC
inhibitors with acyl hydraone moeities in the linker.
[0050] Figure 7 shows exemplary syntheses of intermediates (A, B, and L) useful in
preparing bifunctional HDAC inhibitors.
[0051] Figure 8 shows the synthesis of bifunctional hydroxymates using the
intermediates shown in Figure 7. Dinners may be prepared in parallel For example, over 80
dimers have been synthesized in one day using high-throughput techniques.
[0052] Figure 9 is a western blot showing different activities and selectivities of a
bifunctional hydroxamate and three ortho-hydroxyanilides.
[0053] Figure 10 shows the structures of various bifunctional HDAC inhibitors and their
inhibition of HDAC and TDAC (tubulin deacetylase) at 13 nM The metal chelating
elements (warhead) of the bifunctional inhibitors are joined together as shwon with a 3,4, 5,
6,7, 8,9,10,11, or 12 carbon unit. 4' denotes a 4 carbon unit linker with a trans-double
bond as shown in Figure 10A. Figure 10A shows each of the numbering of each set of
compounds—1-11 for me meta-substituted group with five carbons in the metal chelating
element, 12-22 for the para-substituted group with five carbons in the metal chelating
element, 23-33 for the meta-substituted group with six carbons in the metal chelating
element, and 34-44 for the para-substituted group with six carbons in the metal chelating
element Figures 10B and 10C show the biological activity (HDAC and TDAC inhibitory
acitivify) of these compounds at 13 nM.
[0054] Figure 11 shows the inhibition of HDAC and TDAC activity using one series of
acyl hydrazone-containing bifunctional hydroxamates. These compounds include a para-
substituted phenyl ring in the linker and six carbons in the metal chelating element as shown
in the structure. HDAC and TDAC inhibition are shown at 12.5 nM, 125 nM, and 1100 nM.
These compounds represent selective HDAC inhibitors with better activity than known
HDAC inhibitors

[0055] Figure 12 is a table of data showing the specificity of various bifunctional
hydroxyamates for HDAC versus TDAC. The number of carbons in the metal chelating unit
(warhead), the meta v. para susbstitution pattern, and the number of carbons atoms in the
linker are shown for each compound in the table.
(0056] Figure 13 shows the structures and HDAC and TDAC inhibitory activities of a
control (WT-BM2), a bifunctional hydroxamate (WT-BH37), and a monomeric hydroxamate
compounds (WT-MH2). The bifunctional compound is selective for HDAC whereas the
monomeric compound is not. The control shows no HDAC or TDAC inhibitory activity.
[0057] Figure 14 showsn the catalytic site of an HDAC8 co-crystal structure with an
inhibitor. As shown, the active sites in the crystal structuare are approximately 22 A apart.
As shown in Figure 14C, the metal chelating elements of the bifunctional inventive
compounds are approximately 28 A apart.
[0058] Figure 15 shows the lack of cytotoxicity with the bifunctional hydroxymates in
the RPMI cytotoxicity assay.
[0059] Figure 16 shows how the bifunctional hydroxymates once combined with small
quantities of a cytotoxic agent such as Velcade become cytotoxic.
[0060] Figure 17 demonstrates that bifunctional molecules exhibit potent, selective
activity against HDAC6 function (tubulin deacetylation) in cultured cells.
[0061] Figure 18 is a schematic showing medicinal chemistry optimization of
bifunctional HDAC6 inhibitors. Also pictured are two structures of highly potent, selective
inhibitors of HDAC6.
[0062] Figure 19 shows increased potency and synergy of bifunctional molecule for
HDAC6 in cells compared to other pharmaceutical agents.
[0063] Figure 20 shows a continuous fluorometric biochemical assay for HDAC6
function. Assay is performed in microtiter plate format. Deacetylation of a target substrate
results in the cleavage of the substrate by trypsin, releasing a fluorescent probe. Fluorescent
detection is measured continuously, and enzymatic activity is calculated in the linear range.
[0064] Figure 21 shows a method of determining synergy between compounds. Library
plates are established for each compound (compound 1, yellow), representing dilutions as
indicated. Pin transfer of the library plate of compound 1 and library plate of compound 2
(inverted) establishes the plate map on the right. Four replicates of each compound are
represented, including the full intersecting matrix of all concentrations of both compounds.
This platform can be used rapidly to assemble biological activity data of diverse phenotypes

(cell death, biochemical activity, etc.). Data are then processed using a novel template and
reported using the median effect principle.
[0065] Figure 22 shows the synergy of WT54A and bortezomib in inducing cytotoxicity
in human dexamethasone-sensitive multiple myeloma (MM.1S) cells. Chou-Talalay plot
calculated using the median effect principle. Concentrations of compounds are listed in
micromolar.
[0066] Figure 23 is an exemplary scheme for the synthesis of bifunctional HDAC
inhibitors having a triazole linker formed using the azide-alkyne Huisgen cycloaddition
reaction. Various chelators and warheads may be combined using this chemistry.
[0067] Figure 24 shows five exemplary bifunctional compounds prepared by the
chemistry shown in Figure 23.
Detailed Description of the Invention
[0068] As discussed above, there remains a need for the development of novel
deacetylase inhibitors. In particular HDAC inhibitors that are more potent and/or more
specific than known HDAC inhibitors. HDAC inhibitors specific for a certain class or
member of the HDAC family would be particularly useful both, in the treatment of
proliferative diseases and in the study of HDACs. The present invention provides novel
compounds, and methods for the synthesis thereof, which compounds are useful as inhibitors
of HDACs, and thus are useful for the treatment of proliferative diseases.
Compounds of the Invention
[0069] As discussed above, the present invention provides a novel class of compounds
useful for the treatment of proliferative conditions such as cancer. In certain embodiments,
the compounds of the present invention are useful as inhibitors of histone deacetylases and
thus are useful as anti-cancer 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 (ALL, AML, CML, CLL, etc.), 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. Additionally, 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 foT skin disorders. Examplary skin disorders that
may be treated using the inventive compounds include cutaneous T-cell lymphoma (CTCL),
psoriasis, hair loss, dermatitis, neurofibromatosis, skin pigmentation, etc.
[0070] 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.
[0071] In general, the present invention provides compounds having the general structure
CD:
and pharmaceutically acceptable salts and derivatives thereof;
wherein
A comprises a functional group that inhibits histone deacetylase;
B comprises a functional group that inhibits histone deacetylase, wherein A and B
may be the same or different; and
L is a linker covalently binding together A and B.
[0072] 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
[0073] In certain embodiments, A comprises the formula:

or a salt thereof.


wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, A comprises the formula:

wherein X is O or NH. In certain embodiments, X is O. In other embodiments, X is NH.
[0074] In certain embodiments, A comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or

7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
isNH.
[0075] In certain embodiments, A comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. la other embodiments, X
isNH.
[0076] In certain embodiments, A comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5,6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
isNH.
[0077] In certain embodiments, A comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5,6, or
7. In certain embodiments, A comprises the formula:

wherein X is O or NH. In certain embodiments, X is O. In other embodiments, X is NH.
[0078] In certain embodiments, A comprises the formula:


wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
isNH.
[0079] In certain embodiments, A comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
isNH.
[0080] In certain embodiments, A comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5,6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
isNH.
[0081] 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
0
NH2 ). In other embodiments, A comprises an
comprises an o-aminoanilide (
0
OH ). In yet other embodiments, A comprises a thiol (-
o-hydroxyanilide (
SH).
[0082] In certain embodiments, A comprises the formula:

0 O
N-N^^N-0H
H n H
wherein n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, A comprises the formula:
O 0
wherein n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, A comprises the formula:


0

wherein n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7.


[0083] In certain embodiments, A comprises the formula:
wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2 ; -NHRA'; -NHC(O)RA'; or -
C(RA')3wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; aryltbio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroaryKhio moiety;
m is 0,1,2, 3, or 4; preferably, 0, 1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, n is 6. In certain embodiments, m is 0. In certain embodiments, m is 1.
[0084] In certain embodiments, A comprises the formula:

wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NOz2 -N(RA')2;; -NHRA'; -NHC(O)RA'; or -
C(RA')3> wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl

moiety; alkoxy; aryloxy; alkylthio; aiylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0, 1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5,6, or 7. In certain
emboidments, n is 6. In certain embodiments, m is 0. In other embodiments, m is 1.
[0085] In certain embodiments, A comprises the formula:

wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA, -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
emboidments, n is 6. In certain embodiments, m is 0. In other embodiments, m is 1.
[0086] In certain embodiments, A comprises the formula:


each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA!; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH2. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain emboidments, n is 6. In certain embodiments, m is 0. In other embodiments,
mis 1.
[0087] In certain embodiments, A comprises the formula:

Xis-OH,-SH,or-NH2;
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2;; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2; and

n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH2. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain emboidments, n is 6. In certain embodiments, m is 0. In other embodiments,
mis 1.

wherein
X is-OH,-SH, or-NH2;
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is —NH2. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain emboidments, n is 6. In certain embodiments, m is 0. In other embodiments,
m is 1.


X is -OH, -SH, or -NH2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH2. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain emboidments, n is 6.

wherein
X is -OH, -SH, or-NH2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH2. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain emboidments, n is 6.

wherein
X is -OH, -SH, or -NH2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH2. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain emboidments, n is 6.



wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or-
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0, 1,2, or 3, or 4; preferably, 0, 1, or 2. In certain embodiments, m is 0. In other
embodiments, m is 1.

wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted

wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or-
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0, 1,2, or 3, or 4; preferably, 0, 1, or 2. In certain embodiments, m is 0. In other
embodiments, m is 1.

wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted

or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched orunbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1, 2, or 3, or 4; preferably, 0, 1, or 2. In certain embodiments, m is 0. In other
embodiments, m is 1.
[0096] In certain embodiments, B is a metal chelating functional group. For example, B
is a Zn2+ chelating group. In certain embodiments, B is chosen from the group consisting of:




In certain embodiments, B comprises hydroxamic acid
[0097] In certain embodiments, B comprises the formula:




wherein X is O or NH. In certain embodiments, B comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, B comprises the formula:
wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
is NH.
[0098] In certain embodiments, B comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. in certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
is NH.


[0099] In certain embodiments, B comprises the formula:


wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, X is O. In other embodiments, X is NH. In certain embodiments,
B comprises the formula:



wherein X is O or NH. In certain embodiments, X is O. In other embodiments, X is NH.
[00101] In certain embodiments, B comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5,6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
is NH.
[00102] In certain embodiments, B comprises the formula:

wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, n is 6. In certain embodiments, X is O. In other embodiments, X
is NH.
[00103] In certain embodiments, B comprises the formula:


wherein X is O or NH; and n is an integer between 1 and 20, inclusive; preferably, between 1
and 12, inclusive; more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or
7. In certain embodiments, n is 6. In certain embodiments, X is 0. In other embodiments, X
is NH.
[00104] In other embodiments, B comprises the formula:



In certain particular embodiments, B comprises the formula:



In other embodiments, B comprises a carboxylic acid (-CO2H). In other embodiments, B

comprises an o-aminoanilide (

NH2 ). In other embodiments, B comprises an


OH ). In yet other embodiments, B comprises a thiol (-
o-hydroxyanihde (SH).
[00105] In certain embodiments, B comprises the formula:

wherein n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, B comprises the formula:



wherein n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. 'In certain
embodiments, B comprises the formula:

wherein n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, n is. 6.
[00106] In certain embodiments, B comprises the formula:

wherein
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2; ; -NHRB'; -NHC(O)RB'; or-
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
orheteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5,6, or 7. In certain
embodiments, n is 6. In certain embodiments, m is 0. In certain embodiments, m is 1.

[00107] In certain embodiments, B comprises the formula:

wherein
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB!; -SO2RB'; -NO2; -N(RB')2;; -NHRB'; -NHC(O)RB'; or -
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1, 2, 3, or 4; preferably, 0, 1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, n is 6. In certain embodiments, m is 0. In certain embodiments, m is 1.
[00108] In certain embodiments, B comprises the formula:

wherein
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2; ; -NHRB'; -NHC(O)RB'; or -
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl

moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2,3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, n is 6. In certain embodiments, m is 0. In certain embodiments, m is 1.
[00109] In certain embodiments, B comprises the formula:

wherein
X is-OH,-SH, or-NH`2 `;
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
orunsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2; ; -NHRB'; -NHC(O)RB'; or-
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino., dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0, 1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, n is 5. In other embodiments, n is 6. In certain embodiments, X is -NH`2 `. In
other embodiments, X is -OH. In other embodiments, X is -SH. In certain embodiments, m
is 0. In certain embodiments, m is 1.
[00110] In certain embodiments, B comprises the formula:



wherein
X is-OH,-SH,or-NH`2 `;
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2; ; -NHRB'; -NHC(O)RB'; or-
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a beteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroaryltjio moiety;
m is 0, 1,2, 3, or 4; preferably, 0, 1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH`2 `. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain embodiments, n is 6. In certain embodiments, m is 0. In certain
embodiments, m is 1.
[001111 In certain embodiments, B comprises the formula:

wherein
X is-OH,-SH,or-NH`2 `;
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2;; -NHRB'; -NHC(O)RB'; or-
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl

moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH`2 `. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain embodiments, n is 6. In certain embodiments, m is 0. In certain
embodiments, m is 1.
[00112] In certain embodiments, B comprises the formula:

wherein
X is -OH, -SH, or-NH`2 `; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH`2 `- In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain embodiments, n is 6.
[00113] In certain embodiments, B comprises the formula:

wherein
X is-OH or-NH`2 `; and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH`2 `. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain embodiments, n is 6.
[00114] In certain embodiments, B comprises the formula:



wherein
X is -OH, -SH, or -NH`2 `; and

[00116] In certain embodiments, B comprises the formula:

[00117] In certain embodiments, B comprises the formula:

n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; even more preferably, 5, 6, or 7. In certain
embodiments, X is -NH`2 `. In other embodiments, X is -OH. In other embodiments, X is -
SH. In certain embodiments, n is 6.
[00115] In certain embodiments, B comprises the formula:
wherein
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2;; -NHRB'; -NHC(O)RB'; or-
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl

moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, or 3, or 4; preferably, 0,1, or 2. In certain embodiments, m is 0. In
certain embodiments, m is 1.
[00118] In certain embodiments, B comprises the formula:

wherein
each occurrence of RB is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORB'; -C(=O)RB'; -
CO2RB'; -CN; -SCN; -SRB'; -SORB'; -SO2RB'; -NO2; -N(RB')2; ; -NHRB'; -NHC(O)RB'; or-
C(RB')3; wherein each occurrence of RB' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0, 1,2, or 3, or 4; preferably, 0, 1, or 2. In certain embodiments, m is 0. In
certain embodiments, m is 1.
[00119] ID certain embodiments, A and B are the same. In other embodiments, A and B
are different.
[00120] 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-C20 alkylidene, preferably C1 to C12 alkylidene, more preferably C4-C7

alkylidene. In certein embodiments, L is a a substituted or unsubstituted, cyclic or acyclic,
branched or unbranched heteroaliphatic moiety. In certain embodiments, L comprises a
multicyclic ring system, wherein the rings may be aryl, heteroaryl, non-aromatic carbocyclic,
or non-aromatic heterocyclic. L may comprise 1-20 rings, preferably, 1-10 rings, more
preferably 1-6 rings. These rings may be linked together directed via a covalent bond or via a
aliphatic or heteroaliphatic linker. The rings may also be fused together or spiro-linked. In
other embodiments, L comprises a substituted or unsubstituted aryl moiety. 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 other embodiments, L
comprises a 1,3-dioxane ring; preferably, a trisubstituted 1,3-dioxane ring. In certain
embodiments, L comprises the 1,3-dioxane ring system of tubacin. In certain, embodiments,
L linker provides a spacing of the metal chelating moeities between 20-30 A, preferably, 25-
30 A, more preferably, approximately, 22,23, 24,25, 26,27, 28, or 29 A.
[00121] In certain embodiments, L is of the formula:

wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive:
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive. In certain embodiments, m is 2, 3, 4, 5, 6,7, or 8.
[00122] Tn other embodiments. L is of the formula:

wherein each occurrence of RL' is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, or acyl; and m is an integer between 0 and 20, inclusive; preferably, between
I and 15, inclusive; more preferably, between 1 and 10, inclusvie; even more preferably,
between 1 and 8, inclusive. In certain embodiments, m is 2, 3,4, 5,6, 7, or 8.
[00123] In other embodiments, L is of the formula:



wherein each occurrence of Ar is independently aryl or heteroaryl; and m is an integer
between 0 and 20, inclusive; preferably, between 1 and 15, inclusive; more preferably,
between 1 and 10, inclusvie; even more preferably, between 1 and 8, inclusive. In certain
embodiments, m is 2,3, 4, 5,6, 7, or 8. In certain embodiments, Ar is a monocyclic ring
system (e.g., phenyl, thiazole, imidazole, pyridine, oxazole, pyrrole, etc.). In other
embodimetns, Ar is a bicyclic ring system (e.g., indole, purine, naphthalene., quinoline,
isoquinoh'ne, etc.). Ar may be optionally substituted.
[00124] In other embodiments, L is of the formula:

wherein each occurrence of RL' is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, or acyl; and m is an integer between 0 and 20, inclusive; preferably, between
1 and 15, inclusive; more preferably, between 1 and 10, inclusvie; even more preferably,
between 1 and 8, inclusive. In certain embodiments, m is 2, 3,4,5, 6,7, or 8.

wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive. In certain embodiments, m is 2, 3, 4, 5, 6, 7, or 8.
[00126] In other embodiments, L is of the formula:



wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive. In certain embodiments, m is 2, 3, 4,5,6, 7, or 8.
[00127] In other embodiments. L is of the formula:



wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive. In certain embodiments, m is 2, 3, 4, 5, 6, 7, or 8.
[0012H] In other embodiments. L is of the formula:

wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive. In certain embodiments, m is 2, 3,4, 5,6, 7, or 8.
[001291 In other embodiments, L is of the formula:



wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive. In certain embodiments, m is 2,3,4,5,6, 7, or 8.
[00130] In other embodiments, L is of the formula:

wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive; and each occurrence of RL is independently hydrogen, C1-C6 aliphatic,
heteroaliphatic, aryl, heteroaryl, or acyl. In certain embodiments, RL is acyl. In other
embodiments, RL is hydrogen. In yet other embodiments, RL is C1-C6 alkyl (e.g., methyl). In
certain embodiments, m is 2,3,4,5, 6,7, or 8.


[00131] In other embodiments, L is of the formula:
wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive; and each occurrence of RL, is independently hydrogen, C1-C6 aliphatic,
heteroaliphatic, aryl, heteroaryl, or acyl. In certain embodiments, RL is acyl. In other
embodiments, RL is hydrogen. In yet other embodiments, RL is C1-C6 alkyl (e.g., methyl). In
certain embodiments, m is 2, 3,4, 5, 6, 7, or 8.
[00132] In other embodiments, L is of the formula:

wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive; and each occurrence of RL' is independently hydrogen, C1-C6 aliphatic,
heteroaliphatic, aryl, heteroaryl, alkoxy, ammo, alkylamino, dialkylamino, hydroxy, or thiol.
In certain embodiments, RL' is C1-C6 aliphatic. In other embodiments, RL' is hydrogen. In
yet other embodiments, RL' is C1-C6 alkyl (e.g., methyl). In certain embodiments, m is 2, 3,
4, 5, 6,7, or 8.
[00133] In other embodiments, L is of the formula:

wherein m is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive; and each occurrence of RL' is independently hydrogen, C1-C6 aliphatic,
heteroaliphatic, aryl, heteroaryl, alkoxy, amino, alkylamino, dialkylamino, hydroxy, or thiol.
In certain embodiments, RL' is C1-C6 aliphatic. In other embodiments, RL' is hydrogen. In
yet other embodiments, RL' is C1-C6 alkyl (e.g., methyl). In certain embodiments, m is 2, 3,
4,5,6,7, or 8.
[00134] In other embodiments, L is of the formula:



wherein n is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive.
[00135] In other embodiments, L is of the formula:



[00136] In other embodiments, L is of the formula:



[00137] In other embodiments, L is of the formula:

wherein n is an integer between 0 and 20, inclusive; preferably, between 1 and 15, inclusive;
more preferably, between 1 and 10, inclusvie; even more preferably, between 1 and 8,
inclusive.
[00138] In other embodiments, L is of the formula:

[00139] In other embodiments, L is of the formula:



[00140] In other embodiments, L is of the formula:

wherein
m is an integer between 1 and 4; preferably, between 1 and 2; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA.; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2; ; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety.
[00141] In other embodiments, L is of the formula:

[00142] In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and

each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2; ; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; atkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety. In certain embodiments L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive. In certain
embodiments, both n are equal. In certain other embodiments, both n are different. In certain
embodiments, both n are 1. In certain embodiments, both n are 2. In certain embodiments,
both n are 3.
[00143] In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or a.cyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or "unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2;; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;

aiyloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; c
heteroarylthio moiety. In certain embodiments L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive. In certain
embodiments, both n are equal. In certain other embodiments, both n are different In certain
embodiments, both n are 1. In certain embodiments, both n are 2. In certain embodiments,
both n are 3.
[00144} In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; preferably, between 1
and 3, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2;; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety. In certain embodiments, m is 0. In other embodiments, m is 1. In
certain embodiments, each occurrence of n is 1. In certain embodiments, each occurrence of
n is 2.
[00145] In certain embodiments, L is of the formula:



wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbraached aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2;; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety. In certain embodiments L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive. In certain
embodiments, both n are equal. In certain other embodiments., both n are different. In certain
embodiments, both n are 1. In certain embodiments, both n are 2. In certain embodiments,
both n are 3.
[00146] In certain embodiments, L is of the formula:

wherein
each occurrence of X is independently NH or O;

each occurrence of n is an integer between 1 and 10, inclusive; preferably, between 1
and 3, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -(RA)2;; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylammo, dialkylamino, heteroaryloxy; or
heteroarylthio moiety. In certain embodiments, m is 0. In certain embodiments, m is 1. In
certain embodiments, both occurrences of n are 1. In certain embodiments, both occurrences
of n are 2. In certain embodiments, both X are NH. In other embodiments, both X are O.
[00147] In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA.; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2; ; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety. In certain embodiments L is of the formula:


wherein
each occurrence of n is an integer between 1 and 10, inclusive. In certain
embodiments, both n are equal. In certain other embodiments, both n are different In certain
embodiments, both n are 1. In certain embodiments, both n are 2. In certain embodiments,
both n are 3.
[00148] In certain embodiments, L is of the formula:

wherein
each occurrence of X is independently O or NH;
each occurrence of n is an integer between 1 and 10, inclusive; and
each occurrence of m is an integer between 1 and 10, inclusive. In certain
embodiments, both occurrences of n are 1. In certain embodiments, both occurrences of n are
2. In certain embodiments, both occurrences of n are 3. In certain embodiments, both
occurrences of n are 4. In certain embodiments, both occurrences of m are 1. In certain
embodiments, both occurrences of m are 2. In certain embodiments, both occurrences of m
are 3. In certain embodiments, both occurrences of m are 4. In certain embodiments, the
phenyl ring is para-substituted. In other embodiments, the phenyl ring is meta-substituted. In
yet other embodiments, the phenyl ring is ortho-substituted. The phenyl moiety may also be
optionally substituted. In certain embodiments, both X are NH. In other embodiments, both
X are O.
[00149] In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; and

each occurrence of m is an integer between 1 and 10, inclusive. In certain
embodiments, both occurrences of n are 1. In certain embodiments, both occurrences of n are
2. In certain embodiments, both occurrences of n are 3. In certain embodiments, both
occurrences of n are 4. In certain embodiments, both occurrences of m are 1. In certain
embodiments, both occurrences of m are 2. In certain embodiments, both occurrences of m
are 3. In certain embodiments, both occurrences of m are 4. In certain embodiments, the
phenyl ring is para-substituted. In other embodiments, the phenyl ring is meta-substituted. In
yet other embodiments, the phenyl ring is ortho-substituted. The phenyl moiety may also be
optionally substituted.
[00150] In certain embodiments, L is of the formula:

wherein
each occurrence of X is independently NH or O;
each occurrence of n is an integer between 1 and 10, inclusive; and
m is an integer between 1 and 10, inclusive. In certain embodiments, both
occurrences of n are 1. In certain embodiments, both occurrences of n are 2. In certain
embodiments, both occurrences of n are 3. In certain embodiments, both occurrences of n are
4. In certain embodiments, m is 1. In certain embodiments, m is 2. In certain embodiments,
m is 3. In certain embodiments, m is 4. In certain embodiments, both occurrences of n are 1,
and m is 2. In certain embodiments, both X are O. In other embodiments, both X are NH.
[00151] In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; and
m is an integer between 1 and 10, inclusive. In certain embodiment!:!, both
occurrences of n are 1. In certain embodiments, both occurrences of n are 2. In certain
embodiments, both occurrences of n are 3. In certain embodiments, both occurrences of n are
4. In certain embodiments, m is 1. In certain embodiments, m is 2. In certain embodiments,

m is 3. In certain embodiments, m is 4. In certain embodiments, both occurrences of n are 1,
and m is 2.
[00152] In certain embodiments, L is of the formula:

wherein
each occurrence of X is independently NH or O;
each occurrence of n is an integer between 1 and 10, inclusive; and
each occurrence of m is an integer between 1 and 10, inclusive. In certain
embodiments, both occurrences of n are 1. In certain embodiments, both occurrences of n are
2. In certain embodiments, both occurrences of n are 3. In certain embodiments, both
occurrences of n are 4. In certain embodiments, both occurrences of m are 1. In certain
embodiments, both occurrences of m are 2. In certain embodiments, both occurrences of m
are 3. In certain embodiments, both occurrences of mare 4. In certain embodiments, both X
are NH. In other embodiments, both X are O.
[001531 In certain embodiments, L is of the formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; and
each occurrence of m is an integer between 1 and 10, inclusive. In certain
embodiments, both occurrences of n are 1. In certain embodiments, both occurrences of n are
2. In certain embodiments, both occurrences of n are 3. In certain embodiments, both
occurrences of n are 4. In certain embodiments, both occurrences of m are 1. In certain
embodiments, both occurrences of m are 2. In certain embodiments, both occurrences of m
are 3. In certain embodiments, both occurrences of m are 4.

[00154] In certain embodiments of the invention, compounds of formula (I) are of formula
(Ia):

wherein
L is defined as above.
[00155] In other embodiments of the invention, compound of formula (I) are of formula
(Ib):

wherein
L is defined as above.
[00156] In certain embodiments of the invention, compounds of formula (I) are of the
formula (Ic):


(Ic)
wherein
L is defined as above.
[00157] In certain embodiments of the invention, compounds of formula (I) are of the
formula (Id):


wherein
L is defined as above.
[00158] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
X is O or NH;and
L is defined as above.
[00159] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
X is O or NH;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3,4, 5, 6,7, or 8; preferably, 6,
6, or 7. In certain embodiments, both n are 6.
[00160] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
X is O or NH;

n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3,4,5, 6, 7, or 8; preferably, 6.
[00161] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
X is O or NB;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive;
L is defined as above. In certain embodiments, n is 2,3,4, 5, 6,7, or 8; preferably, 6.
[00162] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
X is Oor NH;
n is an integer between 1 and 20, inclusive; preferably., between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3,4,5,6, 7, or 8; preferably, 6.
[00163] In certain embodiments of the invention, compounds of formula (I) are of the
formula (Ij):

(Ij)
wherein
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and

L is defined as above. In certain embodiments, n is 2,3, 4,5, 6, 7, or 8; preferably, 5
or 6.
[00164] In certain embodiments of the invention, compounds of formula (I) are of the



wherein
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3, 4, 5, 6, 7, or 8; preferably, 5
or 6.
[00165] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SORA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2,3, or 4; preferably, 0,1, or 2;

n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3, 4, 5, 6, 7, or 8; preferably, 5
or 6.
[00166] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of X is -OH or -NH`2 `;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2, 3,4,5,6, 7, or 8; preferably, 5
or 6. In certain embodiments, X is -OH. In other embodiments, X is -NH`2 `.
[00167] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of X is independently -OH or -NH`2 `;
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or "unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a. heteroaryl

moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3, 4, 5, 6, 7, or 8; preferably, 5
or 6. In certain embodiments, X is -OH. In other embodiments, X is -NH`2 `.
[00168] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of X is independently -OH or —NH`2 `;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and


L is defined as above. In certain embodiments, n is 2,3,4,5,6, 7, or 8; preferably, 5
or 6. In certain embodiments, X is -OH. In other embodiments, X is -NH`2 `.
[00169] In certain embodiments of the invention, compounds of formula (I) are of the

[00170] In certain embodiments of the invention, compounds of formula (I) are of the
formula (Iq):

wherein
each occurrence of X is independently -OH or -NH`2 `;
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA'; -C(=O)RA'; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2; ; -NHRA'; -NHC(O)RA'; or -
C(RA')3» wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy;
or heteroarylthio moiety;
m is 0,1,2, 3, or 4; preferably, 0,1, or 2;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and

wherein
each occurrence of X is independently -OH or-NH`2 `;
L is defined as above. In certain embodiments, n is 2,3,4,5, 6,7, or 8; preferably, 5
or 6. In certain embodiments, X is -OH. In other embodiments, X is -NH`2 `.
[00171] In certain embodiments of the invention, compounds of formula (I) are of the

n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3,4, 5,6, 7, or 8; preferably, 5
or 6. 3n certain embodiments, X is -OH. In other embodiments, X is -NH`2 `.
[001721 In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of X is independently -OH or -NH`2 `;
each occurrence of RA is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroary I; -ORA' ; -C(=O)RA' ; -
CO2RA'; -CN; -SCN; -SRA'; -SORA'; -SO2RA'; -NO2; -N(RA')2;; -NHRA'; -NHC(O)RA'; or -
C(RA')3; wherein each occurrence of RA' is independently a hydrogen, a protecting group, an
aliphatic moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl
moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamiao, heteroaryloxy;
or heteroaryKhio moiety;
m is 0,1,2,3, or 4; preferably, 0,1, or 2;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2,3,4, 5, 6, 7, or 8; preferably, 5
or 6. In certain embodiments, X is -OH. In other embodiments, X is -NH`2 `;


[00173] In certain embodiments of the invention, compounds of formula (I) are of the
wherein
each occurrence of X is independently -OH or -NH`2 `;
n is an integer between 1 and 20, inclusive; preferably., between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2, 3,4, 5, 6, 7, or 8; preferably, 5
or 6. In certain embodiments, X is -OH. In other embodiments, X is -NH`2 `.
[00174] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of X is independently -OH or -NH`2 `;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive; and
L is defined as above. In certain embodiments, n is 2, 3,4, 5,6, 7, or 8; preferably, 5
or 6. In certain embodiments, both occurrences of X are -OH. In other embodiments, both
occurrences of X are -NH`2 `.
[00175] In certain embodiments of the invention, compounds of formula (I) are of the


each occurrence of X is independently -OH or -NH`2 `; and
L is defined as above. In certain embodiments, bom occurrences of X are -OH. In
other embodiments, both occurrences of X are -NH`2 `-
[00176] In certain embodiments of the invention, compounds of formula (I) are of the

wherein
each occurrence of X is independently -OH or -NH`2 `; and
L is defined as above. In certain embodiments, both occurrences of X are -OH. In
other embodiments, both occurrences of X are -NH`2 `.
[00177] Certain exemplary compounds of formula (I) include:



[00178] In certain embodiments of the invention, inventive compounds based on the
structure of tubacin are of the formula (II):

wherein
A and B are defined as above; and

R.2 is hydrogen; halogen; cyclic or acyclic, substituted or unsubsrituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORB; -C(=O)RB; -CO2RB; -CN; -SCN; -SRB; -SORB; -SO2RB; -NO2;
-N(RB)2; -NHC(O)RB; or -C(RB)3; wherein each occurrence of RB is independently a
hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, allcylamino,
diallcylamino, heteroaryloxy; or heteroarylthio moiety. In certain embodiments, R2 is
hydrogen. In other embodiments, R2 is hydroxyl or a protected hydroxyl group. In certain
embodiments, R2 is alkoxy. In yet other embodiments, R2 is a lower alkyl, alkenyl, or
alkynyl group. In certain embodiments, R2 is -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, Rz is -CH2-ORB. In other
embodiments, R2 is -CH2-SRB. In yet other embodiments, R2 is -CH2-RB. In other
embodiments, R2 is -CH2-N(RB)2- In still other embodiments, R2 is -CH2-NHRB. In certain
embodiments of the invention, RB is one of:



wherein m and p are each independently integers from 0 to 3; qi is an integer from 1
to 6; R2C is hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R28
is independently hydrogen, halogen, -CN, or WRW1 wherein W is O, S, NRW2, -C(=O), -
S(=O), -SO2, -C(=O)O-, -OC(=O), -CC=O)NRW2, -NRW2C(=O); wherein each occurrence of
RW1 and RW2 is independently hydrogen, a protecting group, a prodrug moiety or an alkyl,
cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is ISIR™2, Rw and
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, RB is one of the structures:



wherein m is an integer from 1 to 4; R20 is hydrogen, lower alkyl or a nitrogen protecting
group; and each occurrence of R2B is independently hydrogen, halogen, -CN, or WRW1
wherein W is O, S, NRW2, -C(=O), -S(=O), -SO2, -C(=O)O-, -OC(=O), -C(=O)NRW2, -
NRW2C(=O); wherein each occurrence of RW1 and RW2 is independently hydrogen, a
protecting group, aprodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl or
heteroaryl moiety, or, when W is NRW2, RW1 and 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.
[00179] In certain embodiments, -X(RB)N has one of the structures:






[00181] In certain embodiments of the invention, the stereochemistry of formula (II) is
chosen from one of the following:

[00182] In certain embodiments of the invention, compounds of formula (II) are of the
formula (IIa):


wherein
A, B, and R2 are defined as above;
X is O or NH;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive. In certain embodiments, n is 2,3,4,5, 6, 7, or 8;
preferably, 6. In certain embodiments, X is NIL In other embodiments, X is O.
[00183] In certain embodiments of the invention, compounds of formula (II) are of the

wnerein
R.2 is defined as above;

n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive. In certain embodiments, n is 2,3,4, 5, 6, 7, or 8;
preferably, 6.
[001841 In certain embodiments of the invention, compounds of formula (II are of the

wherein
R.2 is defined as above.
[00185] In certain embodiments of the invention, compounds of formula (II) are of the




[00186] In certain embodiments of the invention, compounds of formula (II) are of the
[00187] In certain embodiments of the invention, inventive compounds based on the
structure of tubacin are of the formula (III):

wherein
A and B are defined as above;
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive;
each occurrence of m is independently an integer between 0 and 20, inclusive;
preferably, between 0 and 12, inclusive; more preferably between 0 and 8, inclusive;
each occurrence of p is independently 1,2, or 3; and

each occurrence of RL' is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; alkoxy; -CN; -SCN;
alkylthioxy; -NO2; amino, alkylamino, dialkylamino.
[00188] In certain embodiments of the invention, compounds of formula (III) are of the



wherein
A, B, m, n, and RL' are defined as above. In certain embodiments, RL' is hydrogen..
[00189] In another aspect, the invention provides compounds, not necessarily dimer,
multipmeric, or polymeric, that include a acyl hydrazone moiety. The compound are
represented generally by the formula (IV):

and pharmaceutically acceptable salts and derivatives thereof;
wherein
A comprises a functional group that inhibits histone deacetylase;
L is a linker moiety; and
Ro is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic;
cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic;
substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstitued,
branched or unbranched aryl; substituted or unsubstituted, branched or unbranched
heteroaryl.

[00190] 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
other embodiments, A comprises the formula:

or a salt thereof In





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 certain embodiments, A is an acyhydrazone. In
yet other embodiments, A comprises a thiol (-SH).
[00191] In certain embodiments, R0 is substituted or unsubstituted, branched or unbranced
aliphatic. In certain embodiments, R0 is substituted or unsubstituted alkyl. In certain
particular embodiments, R0 is C1-C12 alkyl. In other embodiments, R0 is C1-C6 alkyl. In
certain embodiments, R0 is substituted or unsubstituted alkenyl. In certain embodiments, R0
is substituted or unsubstituted alkynyl. In other embodiments, R0 is substituted or
unsubstituted, branched or unbranced heteroaliphatic.
[00192] In certain embodiments, R0 is arylaliphatic. In other embodiments, R0 is
heteroarylaliphatic. In certain embodiments, R0 is a substituted or unsubstituted aryl moiety.
In certain embodiments, R0 is a monocylic, substituted or unsubstituted aryl moiety,
preferably a five- or six-membered aryl moiety. In other embodiments, R0 is a bicyclic,
substituted or unsubstituted aryl moiety. In still other embodiments, R0 is a tricyclic,
substituted or unsubstituted aryl moiety. In certain embodiments, R0 is a susbstituted or
unsubstituted phenyl moiety. In other embodiments, R0 is a substituted phenyl moiety. In
certain embodiments, R0 is a monosubstituted phenyl moiety. In certain particular
embodiments, R0 is an ortho-substituted R0 moiety. In certain embodiments, R0 is a
substituted or unsubstituted cyclic or heterocyclic.
[00193] In certain embodiments, R0 is a substituted or unsubstituted heteroaryl moiety. In
certain embodiments, R0 is a monocylic, substituted or unsubstituted heteroaryl moiety,
preferably a five- or six-membered heteroaryl moiety. In other embodiments, R0 is a
bicyclic, substituted or unsubstituted heteroaryl moiety. In still other embodiments, R0 is a
tricyclic, substituted or unsubstituted heteroaryl moiety. In certain embodiments, R0
comprises N, S, or O. In certain embodiments, R0 comprises at least one N. In certain
embodiments, R0 comprises at least two N.
[00194] In certain embodiments, R0 is:

wherein

n is an integer between 1 and 5, inclusive; preferably, between 1 and 3, inclusive;
more preferably, 1 or 2;
R1 is is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -CN; -SCN; -SRA; -SORA; -SO2RA; -NO2;
-N(RA)2; ; -NBRA; -NHC(O)RA," or -C(RA)3; wherein each occurrence of RA is independently
a hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; ammo, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety. In certain embodiments, R0 is

wherein
n is an integer between 1 and 4, inclusive; preferably, between 1 and 3, inclusive;
more preferably, 1 or 2;
R1 is is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -CN; -SCN; -SRA; -SOR,.; -SO2RA; -NO2;
-N(RA)2; ; -NHRA; -NHC(O)RA; or -C(RA)3; wherein each occurrence of RA is independently
a hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;

an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety.
[00196] In certain embodiments, R0 is chosen from one of the following:

Any of the above bicyclic ring system may be substituted with up to seven R1 susbstituents as
defined above.
[00197] 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-C20 alkylidene, preferably C1 to C12 alkylidene, more preferably C4-C7
alkylidene. In certain embodiments, L is C1-C20 alkenylidene., preferably d to C12
alkenylidene, more preferably C4-C7 alkenylidene. In certain embodiments, L is C1-C20
alkynylidene, preferably C1 to C12 alkynylidene, more preferably C4-C7 alkynylidene. In
certein 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).

[00198] In certain embodimetns, L is , wherein n is an integer between
1 and 4, inclusive; preferably, between 1 and 3, inclusive; more preferably, 1 or 2; and R1 is
is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA.; -CN; -SCN; -SRA; -SORA; -SO2RA.; -NO2;
-N(RA)2;; -NHRA; -NHC(O)RA; or -C(RA)3; wherein each occurrence of RA is independently
a hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkyltho; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety. Incertain embodiments, L is

[00199] In certain embodiments, L is
[00200] 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


[00202] 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-C6 aliphatic, 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.
[00203] In certain embodiments of the invention, compounds of formula (IV) have the
following structure as shown in formula (IVa):
wherein
n is an integer between 0 and 15, inclusive; preferably, between 0 and 10, inclusive;
more preferably, between 1 and 8, inclusive; even more preferably, 4, 5, 6,7, or 8; and
R0 is defined as above.


[00204] In certain embodiments of the invention, compounds of formula (IV) have the
following structure as shown in formula (IVb):
wherein
n is an integer between 0 and 15, inclusive; preferably., between 0 and 10, inclusive;
more preferably, between 1 and 8, inclusive; even more preferably, 4, 5, 6,7, or 8;
m is an integer between 1 and 5, inclusive; preferably, m is 1, 2, or 3; and
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -CN; -SCN; -SRA; -SORA; -SO2RA.; -NO2;
-N(RA)2; -NHC(O)RA; or -C(RA)3; wherein each occurrence of RA is independently a
hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; ammo, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety. In certain embodiments, R1 is
hydrogen, halogen, hydroxy, ammo, alkylamino, dialkylamino, nitrso, acyl, or C1-C6 alkyl.
In certain embodiments, R1 is aryl. In certain embodiments, R1 is a multicyclic aryl moiety.
In other embodiments, R1 is heteroaryl. In certain embodiments, R1 is carbocyclic. In other
embodiments, R1 is heterocyclic. In certain embodiments R1 comprises a 1,3-dioxane ring
optionally substituted.
[00205] In certain embodiments of the invention, compounds of formula (IV) have the
following stereochemistry and structure as shown in formula (IVc):

wherein
n is an integer between 0 and 15, inclusive; preferably, between 0 and 10, inclusive;
more preferably, between 1 and 8, inclusive; even more preferably, 4, 5, 6,7, or 8; and

R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -CN; -SCN; -SRA; -SORA; -SO2RA; -NO2;
-N(RA)2; -NHC(O)RA; or -C(RA)3; wherein each occurrence of RA is independently a
hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety. In certain embodiments, R1 is
hydrogen, halogen, hydroxy, amino, alkylamino, dialkylamino, nitrso, acyl, or C1-C6 alkyl.
In certain embodiments, R1 is aryl. In other embodiments, R1 is heteroaryl. ID certain
embodiments, R1 is carbocyclic. In other embodiments, R1 is heterocyclic.
[00206] In certain embodiments of the invention, compounds of formula (IV) are of the

wherein
n is an integer between 1 and 5, inclusive; and
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA.; -CN; -SCN; -SRA; -SORA; -SO2RA; -NO2;
-N(RA)2; -NHC(O)RA; or -C(RA)3; wherein each occurrence of RA is independently a
hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety.
[00207] In certain embodiments of the invention, compounds of formula (IV) have the
following stereochemistry and structure as shown in formula (IVe):


wherein
A and L are defined as above;
R2 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORB; -C(=O)RB; -CO2RB; -CN; -SCN; -SRB; -SORB; -SO2RB; -NO2;
-N(RB)2; -NHC(O)RB; or -C(RB)3; wherein each occurrence of RB is independently a
hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety; and
R3 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or

unbranched heteroaryl; -ORc; -C(=O)Rc; -CO2RC; -CN; -SCN; -SRC; -SORc; -SO2Rc; -NO2;
-N(Rc)2; -NHC(O)Rc; or -C(Rc)3; wherein each occurrence of Rc is independently a
hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety, an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety.
[00209] In certain embodiments, R2 is hydrogen. In other embodiments, R2 is hydroxyl or
a protected hydroxyl group. In certain embodiments, R2 is alkoxy. In yet other
embodiments, R2 is a lower alkyl, alkenyl, or alkynyl group. In certain embodiments, R2 is -
CH2-XCRB)n,wherein X is O, S, N, or C, preferably O, S, or N; and n is 1,2, or 3. In certain
embodiments, R2 is -CH2-ORB. In other embodiments, R2 is -CH2-SRB. In yet other
embodiments, R2 is -CH2-RB. In other embodiments, R2 is -CH2-N(RB)2- In still other
embodiments, R2 is -CH2-NHRB. In certain embodiments of the invention, EB is one of:



wherein m and p are each independently integers from 0 to 3; q1 is an integer from 1
to 6; R2C is hydrogen, lower alkyl or a nitrogen protecting group; and each occurrence of R2B
is independently hydrogen, halogen, -CN, or WRW1 wherein W is O, S, NRW2, -C(=O), -
S(=O), -SO2) -C(=O)O-, -OC(=O), -C(=O)NRW2, -NRW2C(=O); wherein each occurrence of
RW1 and Rw2 is independently hydrogen, a protecting group, a prodrug moiety or an alkyl,.
cycloalkyl, heteroalkyl, heterocyclic, aryl or heteroaryl moiety, or, when W is NRW2, RW1 and
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, RB is one of the structures:



wherein m is an integer from 1 to 4; R2C is hydrogen, lower alkyl or a nitrogen protecting
group; and each occurrence of R28 is independently hydrogen, halogen, -CN, or WRW1
wherein W is O, S, NRW2, -C(=O), -S(=O), -SO2,-C(=O)O-, -OC(=O), -C(=O)NRW2, -
NRW2C(=O); wherein each occurrence of RW1 and R"2 is independently hydrogen, a
protecting group, a prodrug moiety or an alkyl, cycloalkyl, heteroalkyl, heterocyclic, aryl o:
heteroaryl moiety, or, when W is NRW2, RW1 and 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.
[00210] In certain embodiments, -X(RB)n has one of the structures:






and Y is NH, S, or 0. In other embodiments, R2 is
[00212] In certain embodiments, R3 is substituted or unsubstituted aryl. In certain
embodiments, R3 is substituted or unsubstituted phenyl. In certain particular embodiments,R3
is monosubstituted phenyl. In certain embodiments, R3 is para-substituted phenyl In certain

solid support unit, an alkyl, acyl, cycloalkyl, heteroalkyl, heterocyclic, aryl, heteroaryl, -
(alkyl)aryl, -(alkyl)heteroaryl, -(heteroalkyl)aryl, or -(heteroalkyl)heteroaryl moiety. In

or unsubstituted heteroaryl.
[00213] In certain embodiments, the stereochemistry of formula (IVf) is defined as
follows:


[00214] 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.
[00215] 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.
[00216] Compounds of the invention may be prepared by crystallization of compound of
any of the formula above under different conditions and may exist as one or a combination of
polymorphs of compound of any general formula above 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
[00217] The synthesis of the various monomeric compounds used to prepare the
bifunctional, multifunctional, and polyfunctional compounds of the invention are known in
the art. These published syntheses may be utilized to prepare the compounds! of the
invention. In one embodiment, the monomeric units are prepared or obtained and two of
more of the units are linked together using linker known in the art. In certain embodiments,
functional groups on the monomeric units may be activated to form a covalent attachment
with the linker moiety. In other embodiments, an activated functional group on the linker is
used to form a covalent attachment to the monomeric unit In certain embodiments, the bond
formed is an ester or amide bond. The syntheses of the monomeric units used in preparing
the inventive bifunctional or multifunctional compounds are described in US 6,960,685; US
6,897,220; US 6,541,661; US 6,512,123; US 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.
[00218] In certain emobidments, a bifunctional linker moiety is reacted with two
equivalents of monomeric units. In certain specific embodiments, the bifunctional linker

includes two activated eletrophilic moieties such as activated esters. The electrophilic
moieties are reacted with a nucleophilic moiety of the monomeric unit as shown below. In
certain specific embodiments, the bifunctional linker includes two aldhyde moieities which
are reacted with a hydrazine moiety of the monomeric unit. In other embodiments, the
bifunctional linker includes two nucleophilic moieties (e.g., thiols, alcohols, amines). The
nucleophilic moieties are reacted with electrophiles of the monomeric units. In certan
embodiments, the electrophiles is an actived acyl moiety. As would be appreciated by one of
skill in this art various of functional groups of the bifunctional linker and/or monomeric units
may be optionally protected.

[00219] In certain embodiments, the inventive bifunctional compounds are constructed
using click chemistry (e.g., Huisgen 1,3-dipolar cycloaddtion; Diels-Alder reaction; other
cylcoaddition reactions; nucleophilic substitution; urea formation, amide formation, ester
formation; epoxide opening; etc.). In certain particular embodiments, the bifunctional
compounds are constructed using the azide-alkyne Huisgen 1,3-cycloaddition reaction as
shown below. For example the monomeric unit may contain a alkynyl moiety that is reacted
with an azide moiety of the bifunctional linker to form a triazole moiety. In other
embodiments, the monomeric unit includes the azide moiety, and the bifunctional linker
includes the alkynyl moiety. As would be appreciated by those of skill in the art, various
functional groups of the linker and/or monomeric units may be optionally protected during
the cycloaddition reaction and subsequently deprotected.

[00220] Exemplary syntheses of bifunctional HDAC inhibitors are shown in Figures 7, 8,
and 23.

Pharmaceutical Compositions
[00221] 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.
[00222] 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 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.
[00223] 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.
[00224] As used herein, the term "pharmaceutically acceptable salt" refers to those salts
which are, within the scope of sound medical judgment, suitable for use in contact with the
tissues of humans and lower animals without undue toxicity, irritation, allergic response and
the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically
acceptable salts of amines, carboxylic acids, and other types of compounds, are well known
in the art. For example, S.M. Berge, et al. describe pharmaceutically acceptable salts in
detail in J. Pharmaceutical Sciences, 66:1-19 (1977), incorporated herein by reference. The
salts can be prepared in situ during the final isolation and purification of the compounds of

the invention, or separately by reacting a free base or free acid function with a suitable
reagent, as described generally below. For example, a free base function can be reacted with a
suitable acid. Furthermore, where the compounds of the invention carry an acidic moiety,
suitable pharmaceutically acceptable salts thereof may, include metal salts such as alkali
metal salts, e.g. sodium or potassium salts; and alkaline earth metal salts, e.g. calcium or
magnesium salts. Examples of pharmaceutically acceptable, nontoxic acid addition salts are
salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic
acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic
acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by
using other methods used in the art such as ion exchange. Other pharmaceutically acceptable
salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,
borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate,
dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate,
gluconate, hernisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate,
lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-
naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate,
persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate,
sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like.
Representative alkali or alkaline earth metal salts include sodium, lithium, potassium,
calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when
appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using
counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl
sulfonate and aryl sulfonate.
[00225] Additionally, as used herein, the term "pharmaceutically acceptable ester" refers
to esters that hydrolyze in vivo and include those that break down readily in the human body
to leave the parent compound or a salt thereof. Suitable ester groups include, for example,
those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularly
alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl
moeity advantageously has not more than 6 carbon atoms. Examples of particular esters
include formates, acetates, propionates, butyrates, acrylates and ethylsuccinates.
[00226] 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.
[00227] 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.
[00228] Liquid dosage forms for oral administration include, but are not limited to,
pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and

elixirs. In addition to the active compounds, the liquid dosage forms may contain inert
diluents commonly used in the art such as, for example, water or other solvents, solubilizing
agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate,
benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide,
oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils),
glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan,
and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants
such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and
perfuming agents.
[00229] Injectable preparations, for example, sterile injectable aqueous or oleaginous
suspensions may be formulated according to the known art using suitable dispersing or
wetting agents and suspending agents. The sterile injectable preparation may also be a sterile
injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or
solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and
solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium
chloride solutioa In addition, sterile, fixed oils are conventionally employed as a solvent or
suspending medium. For this purpose any bland fixed oil can be employed including
synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the
preparation of injectables.
[00230] The injectable formulations can be sterilized, for example, by filtration through a
bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid
compositions which can be dissolved or dispersed in sterile water or other sterile injectable
medium prior to use.
[00231] In order to prolong the effect of a drug, it is often desirable to slow the absorption
of the drug from subcutaneous or intramuscular injection. This may be accomplished by the
use of a liquid suspension or crystalline or amorphous material with poor water solubility.
The rate of absorption of the drug then depends upon its rate of dissolution that, in turn, may
depend upon crystal size and crystalline form. Alternatively, delayed absorption of a
parenterally administered drug form is accomplished by dissolving or suspending the drug in
an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the
drug in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio
of drug to polymer and the nature of the particular polymer employed, the rate of drug release
can be controlled. Examples of other biodegradable polymers include (poly(orthoesters) and

poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in
liposomes or microemulsions which are compatible with body tissues.
[00232] Compositions for rectal or vaginal administration are preferably suppositories
which can be prepared by mixing the compounds of this invention with suitable non-irritating
excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which
are solid at ambient temperature but liquid at body temperature and therefore melt in the
rectum or vaginal cavity and release the active compound.
[00233] Solid dosage forms for oral administration include capsules, tablets, pills,
powders, and granules. In such solid dosage forms, the active compound is mixed with at
least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or
dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose,
mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates,
gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d)
disintegrating agents such as agar—agar, calcium carbonate, potato or tapioca starch, alginic
acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f)
absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as,
for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and
bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid
polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules,
tablets and pills, the dosage form may also comprise buffering agents.
[00234] Solid compositions of a similar type may also be employed as fillers in soft and
hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high
molecular weight polyethylene glycols and the like. The solid dosage forms of tablets,
dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric
coatings and other coatings well known in the pharmaceutical formulating art. They may
optionally contain opacifying agents and can also be of a composition that they release the
active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally,
in a delayed manner. Examples of embedding compositions that can be used include
polymeric substances and waxes. Solid compositions of a similar type may also be employed
as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar
as well as high molecular weight polethylene glycols and the like.
[00235] The active compounds can also be in micro-encapsulated form with one or more
excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and
granules can be prepared with coatings and shells such as enteric coatings, release controlling

coatings and other coatings well known in the pharmaceutical formulating art. In such solid
dosage forms the active compound may be admixed with at least one inert diluent such as
sucrose, lactose and starch. Such dosage forms may also comprise, as in normal practice,
additional substances other than inert diluents, e.g., tableting lubricants and other tableting
aids such as magnesium stearate and microcrystalline cellulose. In the case of capsules,
tablets and pills, the dosage forms may also comprise buffering agents. They may optionally
contain opacifying agents and can also be of a composition that they release the active
ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a
delayed manner. Examples of embedding compositions which can be used include polymeric
substances and waxes.
[00236] 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, burylated 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.
[00237] In certain embodiments, the pharmaceuticaily 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. L 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, III. (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-methyl pyrrolidone.
[00238] 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 pharmaceuticaily 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.
[00239] 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).
[00240] 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, y-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-Fluprouracil, 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 (CM) 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).
[00241] 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).
[00242] 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.
[00243] 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
[00244] 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 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.
[00245] 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);
• exhibitthe ability to inhibit HDAC2 (Genbank Accession No. NP 001.518,
incorporated herein by reference);
• exhibit the ability to inhibit HDAC3 (Genbank Accession No. 015739, 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 0060355
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 deacectylase (TD AC);
• 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/or

• exhibit a therapeutic profile (e.g., optimum safety and curative effect) that is superior
to existing chemotherapeutic agents.
[00246] As detailed in the exemplification herein, in assays to determine the ability of
compounds to inhibit cancer cell growth certain inventive compounds may exhibit IC50
values ≤ 100 µM. In certain other embodiments, inventive compounds exhibit IC50 values ≤
50 µM. In certain other embodiments, inventive compounds exhibit IC50 values ≤ 40 µM. In
certain other embodiments, inventive compounds exhibit IC50 values ≤ 30 µM. In certain
other embodiments, inventive compounds exhibit IC50 values ≤ 20 µM. In certain other
embodiments, inventive compounds exhibit ICso values ≤ 10 uM. In certain other
embodiments, inventive compounds exhibit ICso values ≤ 7.5 uM. In certain embodiments,
inventive compounds exhibit ICso values ≤ 5 µM. In certain other embodiments, inventive
compounds exhibit IC50 values ≤ 2.5 µM. In certain embodiments, inventive compounds
exhibit ICso values ≤ 1 µM. In certain embodiments, inventive compounds exhibit IC50 values
≤ 0.75 µM. In certain embodiments, inventive compounds exhibit IC50 values ≤ 0.5 µM. In
certain embodiments, inventive compounds exhibit IC50 values ≤ 0.25 µM. In. certain
embodiments, inventive compounds exhibit IC50 values ≤ 0.1 µM. In certain other
embodiments, inventive compounds exhibit IC50 values ≤ 75 nM. In certain other
embodiments, inventive compounds exhibit IC50 values ≤ 50 nM. In certain other
embodiments, inventive compounds exhibit IC50 values ≤ 25 nM. In certain other
embodiments, inventive compounds exhibit IC50 values ≤ 10 nM. In other embodiments,
exemplary compounds exhibited ICso values ≤ 7.5 nM. In other embodiments, exemplary
compounds exhibited IC50 values ≤ 5 nM.
Pharmaceutical Uses and Methods of Treatment
[00247] 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. As discussed above, the compounds of the invention are selective
inhibitors of histone deacetylases and, as such, are useful in the treatment of disorders
modulated by histone deacetylases. For example, compounds of the invention may be useful
in the treatment of cancer. 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.
[00248] 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 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.
[00249] 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).
[00250] 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.

[00251] 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 US Patents 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. Patent 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.
[00252] 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.
[00253] 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.
[00254] 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 Publication No.: 2003/0004209 in paragraphs
[0146]-[0155], which is hereby incorporated herein by reference.
[00255] 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 the
invention or a composition comprising said compound.
[00256] 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 theraDeutic agents.

[00257] 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.
[00258] 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.
[00259] The compounds of the invention are preferably formulated in dosa.ge 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).
[00260] 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 a compound of formula
I or a composition comprising said compound.
[00261] 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.
Assay
[00262] In another aspect, the invention provides a biochemical assay for identifying
inhibitors of deacetylase activity. The assay may be performed in a high-throughput format
For example, the assay may be performed in a multi-well plate format. The assay may be
modified to screen for inhibitors of particular HDACs or TDACs. In certain embodiments,
the assay is used to identify inhibitors of HDAC1, HDAC2, HDAC3, HDAC4, HDAC5,
HDAC6, HDAC7, HDAC8, HDAC9, HDAC10, or HDAC11. In certain embodiments,
HDAC6 is used in the assay. Test compounds may be screened against multiple HDACs in
order to determine their selectivity. A target substrate is incubated with an HDAC or other
protein with deacetylase activity in the presence of a test compound. In certain embodiments,
the target substrate includes an acetylated lysine residue. Deacetylation of the substrate
allows trypsin or another protease to cleave the substrate, thereby releasing a fluorescent
probe. Fluorescence can be continuously monitored in order to determine the ability of the
test compound to inhibit the deacetylation activity. The HDAC or other enzyme may be
purified or used crude in the inventive assay. In certain embodiments, the assay is a cell-free
assay. The assay is illustrated in Figure 20.
Treatment Kit
[00263] 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 delivery of solid oral forms such as tablets or capsules. Such a kit preferably

includes a number of unit dosages, and may also include a card having the dosages oriented
in the order of their intended use. If desired, a memory aid can be provided, for example in
the form of numbers, letters, or other markings or with a calendar insert, designating the days
in the treatment schedule in which the dosages can be administered. Alternatively, placebo
dosages, or calcium dietary supplements, either in a form similar to or distinct from the
dosages of the pharmaceutical compositions, can be included to provide a kit in which a
dosage is taken every day. 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
[00264] 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. If 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.
[00265] 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
[00266] 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.

Example 1: Synthetic Methods
[00267] 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.
[00268] Moreover, the practitioner is directed to the specific guidance and examples
provided in this document relating to various exemplary compounds and intermediates
thereof
[00269] 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.
[00270] 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.
[00271] 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, WI), Bachem (Torrance, CA), 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, NY, 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, NY, 1991; March 2001,
"Advanced Organic Chemistry", 5th ed. John Wiley and Sons, New York, NY; and Larock
1990, "Comprehensive Organic Transformations: A Guide to Functional Group
Preparations", 2nd ed. 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.

[00272] 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.
Example 2: Biological Assay Procedures
[00273] Cell culture and Transfections. TAg-Jurkat cells were transfected by
electroporation with 5 ug of FLAG-epitope-tagged pBJ5 constructs for expression of
recombinant proteins. Cells were harvested 48 h posttransfection.
[00274] HDAC assays. [3H]Acetate-incorporated histones were isolated from butyrate-
treated HeLa cells by hydroxyapatite chromatography (as described in Tong, et al. Nature
1997, 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., Science 1996, 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.
Example 3: In vivo activity
[00275] 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 mm3 after 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.

Example 4: Assays to identify potential antiprotozoal compounds by inhibition of
histone deacetylase
[00276] As detailed in US Patent Number 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 6,068,987 are hereby incorporated by reference.

Claims

wherein
A comprises a functional group that inhibits histone deacetylase;
B comprises a functional group that inhibits histone deacetylase, wherein A and B
may be the same or different; and
L is a linker covalently binding together A and B; and pharmaceutically acceptable
salts thereof.
2. The compound of claim 1, wherein A and B are functional groups that chelate Zn2+.
3. The compound of claim 1, wherein A and B are selected from the group consisting of:

4. The compound of claim 1,2 or 3, wherein A and B are the same.
5. The compound of claim 1, 2, or 3, wherein A and B are different.


12. The compound of any one of claims 1-11, wherein 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.
13. The compound of any one of claims 1-11, wherein L is of the formula:



wherein m is an integer between 0 and 20, inclusive.
14. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
each occurrence of RL is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, or acyl; and
m is an integer between 0 and 20, inclusive.
15. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
each occurrence of Ar is independently aryl or heteroaryl; and
m is an integer between 0 and 20, inclusive.
16. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
each occurrence of RL' is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, or acyl; and
m is an integer between 0 and 20, inclusive.
17. The compound of any one of claims 1-11, wherein L is of the formula:



wherein
m is an integer between 0 and 20, inclusive.
18. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
m is an integer between 0 and 20, inclusive.
19. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
m is an integer between 0 and 20, inclusive.
20. The compound of any one of claims 1-11, wherein L is of the formula:



wherein m is an integer between 0 and 20, inclusive.
21. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
m is an integer between 0 and 20, inclusive.
22. The compound of any one of claims 1-11, wherein L is of the formula:


wherein
m is an integer between 0 and 20, inclusive; and
each occurrence of RL is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, or acyl.
23. The compound of claim 22, wherein RL is acetyl.
24. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
m is an integer between 0 and 20, inclusive; and
each occurrence of RL is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, or acyl.
25. The compound of any one of claims 1-1L wherein L is of the formula:

wherein
m is an integer between 0 and 20, inclusive; and
each occurrence of RL' is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, alkoxy, amino, alkylamino, dialkylamino, hydroxy, or thiol.
26. The compound of any one of claims 1-11, wherein L is of the formula:

wherein
m is an integer between 0 and 20, inclusive; and

each occurrence of RL' is independently hydrogen, C1-C6 aliphatic, heteroaliphatic,
aryl, heteroaryl, alkoxy, amino, alkylamino, dialkylamino, hydroxy, or thiol.
27. The compound of any one of claims 1-11, whereinL is of formula:



28. The compound of any one of claims 1-11, wherein L is of formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unstibstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(==O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2; ; -NHRA; -NHC(O)RA; or-C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylarnino, heteroaryloxy; or
heteroarylthio moiety.
29. The compound of any one of claims 1-11, wherein L is of formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and

each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched orunbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2; ; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety.
30. The compound of any one of claims 1-11, wherein L is of formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2; ; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety.
31. The compound of any one of claims 1-11, wherein L is of formula:


wherein
each occurrence of n is an integer between 1 and 10, inclusive;
m is an integer between 1 and 4, inclusive; preferably, between 1 and 2, inclusive; and
each occurrence of R1 is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; -ORA; -C(=O)RA; -CO2RA; -
CN; -SCN; -SRA; -SORA; -SO2RA; -NO2; -N(RA)2;; -NHRA; -NHC(O)RA; or -C(RA)3;
wherein each occurrence of RA is independently a hydrogen, a protecting group, an aliphatic
moiety, a heteroaliphatic moiety, an acyl moiety; an aryl moiety; a heteroaryl moiety; alkoxy;
aryloxy; alkylthio; arylthio; amino, alkylamino, dialkylamino, heteroaryloxy; or
heteroarylthio moiety.
32. The compound of any one of claims 1-11, wherein L is of formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; and
each occurrence of m is an integer between 1 and 10, inclusive.
3 3. The compound of any one of claims 1-11, wherein L is of formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; and
m is an integer between 1 and 10, inclusive.

34. The compound of any one of claims 1-11. wherein L is of formula:

wherein
each occurrence of n is an integer between 1 and 10, inclusive; and
each occurrence of m is an integer between 1 and 10, inclusive.
35. The compound of any one of claims 1 and 12-34 of formula (Ia):

36. The compound of any one of claims 1 and 12-34 of formula (Ib):

37. The compound of any one of claims 1 and 12-34 of formula (Ic):

38. The compound of any one of claims 1 and 12-34 of formula (Id):



39. The compound of anv one of claims 1 and 12-34 of formula (Ie):



40. The compound of any one of claims 1 and 12-34 of formula (If):



wherein
X is O or NH;and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive.
41. The compound of any one of claims 1 and 12-34 of formula (Ig):

wherein
X is O or NH;and
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive.
42. The compound of any one of claims 1 and 12-34 of formula (Ih):


wherein
X is O or NH; and
n is an integer between 1 and 20, inclusive.
43. The compound of any one of claims 1 and 12-34 of formula (Ii):

wherein
X is O or NH; and
n is an integer between 1 and 20, inclusive.
44. The compound of claim 40,41,42, or 43, wherein n is 6.
45. The compound of claim 39,40,41, 42, or 43, wherein X is NH.
46. The compound of claim 39,40,41,42, or 43, wherein X is O.
47. The compound of claim 1 of one of the formulae:




wherein
R2 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or
unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; siibstituted or
unsubstitued, branched or unbranched aryl; substituted or unsubstituted, branched or
unbranched heteroaryl; -ORB; -C(=O)RB; -CO2RB; -CN; -SCN; -SRB; -SORB; -SO2RB; -NO2;
-N(RB)2;; -NHRB; -NHC(O)RB; or -C(RB)3; wherein each occurrence of RB is independently
a hydrogen, a protecting group, an aliphatic moiety, a heteroaliphatic moiety., an acyl moiety;
an aryl moiety; a heteroaryl moiety; alkoxy; aryloxy; alkylthio; arylthio; amino, alkylamino,
dialkylamino, heteroaryloxy; or heteroarylthio moiety.
49. The compound of claim 48, wherein R2 is -CH2-X(RB)n, wherein X is O, S, N, or C;
and n is 1,2, or 3.
50. The compound of claim 48, wherein R2 is -CH2-ORB.
51. The compound of claim 48, wherein R2 is -CH2-SRB.
52. The compound of claim 48, wherein R2 is -CH2-N(RB)2.
53. The compound of claim 52, wherein the two RB groups form a cyclic structure.
54. The compound of claim 48, wherein R2 is -CH2-NHRB.
55. The compound of any one of claims 48-54 of one of the formulae:



wherein
X is O or NH;
n is an integer between 1 and 20, inclusive.
57. The compound of any one of claims 48-54 of the formula (IIb):


wherein
n is an integer between 1 and 20, inclusive.
58. The compound of claim 48 of formula:



wherein
n is an integer between 1 and 20, inclusive; preferably, between 1 and 12, inclusive;
more preferably between 2 and 8, inclusive;
each occurrence of m is independently an integer between 0 and 20, inclusive;
preferably, between 0 and 12, inclusive; more preferably between 0 and 8, inclusive;
each occurrence of p is independently 1,2, or 3; and
each occurrence of RL' is independently hydrogen; halogen; cyclic or acyclic,
substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted
or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted,
branched or unbranched acyl; substituted or unsubstitued, branched or unbranched aryl;
substituted or unsubstituted, branched or unbranched heteroaryl; alkoxy; -CN; -SCN;
alkylthioxy; -NO2; amino, alkylamino, dialkylamino.
61. The compound of claim 59 or 60, wherein m is 6.
60. The compound of claim 59 of the formula (IIIa):


62. The compound of claim 59,60, or 61, wherein n is 4, 5, 6, or 7.
63. A compound of formula:

and pharmaceutically acceptable salts and derivatives thereof;
wherein
A comprises a functional group that inhibits histone deacetylase;
L is a substituted or unsubstitated, 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.; and
R0 is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic;
cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic;
substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstitued,
branched or unbranched aryl; substituted or unsubstituted, branched or unbranched
heteroaryl.
64. A pharmaceutical composition comprising a compound of one of the claims 1-63 and a
pharmaceutically acceptable excipient.
65. The pharmaceutical composition of claim 64 further comprising a cytotoxic agent.

66. A method of inhibiting histone deacetylase, the method comprising steps of:
contacting a histone deacetylase with a compound of one of the claims 1-63.
67. The method of claim 66, wherein the histone deacetylase is purified.
68. The method of claim 66, wherein the histone deacetylase is in a cell.
69. The method of claim 66, wherein the histone deacetylase is HDAC6.

70. A method of treating a subject with a proliferative disorder, the method comprising
steps of:
administering a therapeutically effective amount of a compound of one of claims 1-54
to a subject.
71. The method of claim 70, wherein the subject is a mammal.
72. The method of claim 70, wherein the subject is human.
73. The method of claim 70, 71, or 72, wherein the proliferative disorder is cancer.
74. The method of claim 70, 71, or 72, wherein the proliferative disorder is an
inflammatory disease.
75. A method of indentifying inhibitors of histone deacetylases (HDACs), the method
comprising steps of:
providing a test compound;
contacting the test compound with a histone deacetylase (HDAC) in the presence of a
target substrate, wherein the deacetylated form of the target substrate is cleaved by trypsin to
release a fluorescent probe; and
measuring the fluorescence of the released fluorescent probe.
76. The method of claim 75, wherein the HDAC is HDAC 6.
77. The method of claim 75 or 76, wherein the target substrate comprises an acetylated
lysine residue.
78. The method of claim 75, wherein the step of contacting comprises contacting the test
compound with at least two histone deactylases.
79. The method of claim 75,76, or 78, wherein the fluorescent probe is of formula:



80. A method of preparing a compound of claim 1, the method comprising steps:
reacting a bifunctional compound of formula:

wherein
L is a linker; and
X is a leaving group;
with a nucleophile of formula:

wherein
Nu is nucleophile; and
A comprises a functional group that inhibits histone deacetylase; under suitable
conditions to form a compound of formula:



81. The method of claim 80, wherein the step of reacting comprises reacting the
bifunctional compound with at least two equivalents of the nucleophile.
82. A method of preparing a compound of claim 1, the method comprising steps:
reacting a bifunctional compound of formula:

wherein
L is a linker;
with an alkyne of formula:

wherein

A comprises a functional group that inhibits histone deacetylase; under suitable
conditions to form a compound of formula:

83. The method of claim 82, wherein the step of reacting comprises reacting the
bimnctional compound with at least two equivalents of the alkyne.
84. The method of claim 82 or 83, wherein the step of reacting comprises reacting in the
presence of copper (I).

In recognition of the need to develop novel therapeutic agents and efficient methods for the
synthesis thereof, the present invention
provides novel bifunctional, trifunctional,
or multifunctional compounds for inhibiting histone deacetylases, and pharmaceutically acceptable salts and derivatives thereof. The present invention further provides methods for treating disorders regulated by histone deacetylase activity (e.g., proliferative diseases, cancer, inflammatory diseases, protozoal infections, hair loss, etc.) comprising
administering a therapeutically effective
amount of an inventive compound to a subject in need thereof. The present invention also provides methods for preparing compounds of the invention.

Documents:

http://ipindiaonline.gov.in/patentsearch/GrantedSearch/viewdoc.aspx?id=E7D6rKQTbwD2WwbLasJdVA==&loc=wDBSZCsAt7zoiVrqcFJsRw==


Patent Number 272514
Indian Patent Application Number 3512/KOLNP/2008
PG Journal Number 15/2016
Publication Date 08-Apr-2016
Grant Date 05-Apr-2016
Date of Filing 28-Aug-2008
Name of Patentee DANA-FARBER CANCER INSTITUTE. INC
Applicant Address 44 BINNEY STREET, BOSTON, MA 02115 UNITED STATES OF AMERICA
Inventors:
# Inventor's Name Inventor's Address
1 BRADNER, JAMES, ELLIOT 129 FRANKLIN STREET, APT. 317, MA
2 TANG, WEIPING 60 WADSWORTH STREET, APT. 5E, CAMBRIDGE, MA 02142
3 SCHREIBER, STUART, L. 2 AVERY STREET #1E, BOSTON, MA 02111
4 MAZITSCHEK, RALPH 43 GLENWOOD ROAD, SOMERVILLE, MA 02145
PCT International Classification Number A61K 38/00
PCT International Application Number PCT/US2007/062145
PCT International Filing date 2007-02-14
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/773510 2006-02-14 U.S.A.