A Structural Insight into Hydroxamic Acid Based ...

2 downloads 137 Views 3MB Size Report
droxamic acid based HDACi i.e., belinostat, abexinostat, SB939, resminostat, givinostat, quisinostat, pentobinostat,. CUDC-101 are in clinical trials and one of ...
Send Orders for Reprints to [email protected] Current Medicinal Chemistry, 2014, 21, ????-????

1

A Structural Insight into Hydroxamic Acid Based Histone Deacetylase Inhibitors for the Presence of Anticancer Activity H. Rajak*,1, A. Singh1, K. Raghuwanshi1, R. Kumar1, P.K. Dewangan1, R. Veerasamy2, P.C. Sharma3, A. Dixit4 and P. Mishra5 1

Medicinal Chemistry Research Laboratory, SLT Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur-495 009, (CG) India; 2Faculty of Pharmacy, AIMST University, Semeling, 08100 Bedong, Kedah Darul Aman, Malaysia; 3Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra-136 119, (Haryana) India; 4 Institute of Life Sciences, Bhubaneswar-751 001, (Orissa) India; 5Institute of Pharmaceutical Sciences and Research, GLA University, Mathura-281 406, (UP) India Abstract: Histone deacetylase inhibitors (HDACi) have been actively explored as anti-cancer agents due to their ability to prevent deacetylation of histones, resulting in uncoiling of chromatin and stimulation of a range of genes associated in the regulation of cell survival, proliferation, differentiation and apoptosis. During the past several years, many HDACi have entered pre-clinical or clinical research as anti-cancer agents with satisfying results. Out of these, more than 8 novel hydroxamic acid based HDACi i.e., belinostat, abexinostat, SB939, resminostat, givinostat, quisinostat, pentobinostat, CUDC-101 are in clinical trials and one of the drug vorinostat (SAHA) has been approved by US FDA for cutaneous Tcell lymphoma (CTCL). It is clear from the plethora of new molecules and the encouraging results from clinical trials that this class of HDAC inhibitors hold a great deal of promise for the treatment of a variety of cancers. In this review, we classified the hydroxamic acid based HDACi on the basis of their structural features into saturated, unsaturated, branched, un-branched and 5, 6-membered cyclic ring linker present between zinc binding group and connecting unit. The present article enlists reports on hydroxamic acid based HDACi designed and developed using concepts of medicinal chemistry, demonstrating that hydroxamate derivatives represent a versatile class of compounds leading to novel imaging and therapeutic agents. This article will also provide a complete insight into various structural modifications required for optimum anticancer activity.

Keywords: Anticancer agents, belinostat, givinostat, histone, histone deacetylase inhibitors, hydroxamic acid, panobinostat, vorinostat. 1. INTRODUCTION Histone deacetylase inhibitors (HDACi) have been proven to be effective therapeutic agents to kill cancer cells through inhibiting histone deacetylase (HDAC) activity or altering the structure of chromatin. Chromatins are composed of nucleosomes which contain histone proteins, nonhistone chromosomal proteins (positively charged), RNA and are winded by DNA which are negatively charged. Chromatin can be present in the nucleus as heterochromatin, highly compact and transcriptionally inactive and euchromatin, accessible to RNA polymerases for transcriptional processes and gene expression. A nucleosome comprises of 146 nucleotide base pairs of DNA wrapped around the core histone octamer, which is composed of two copies each of H2A, H2B, H3, and H4 proteins. These proteins are basic due to the amino-terminal side chains rich in the amino acid lysine [1-3]. The acetylation and deacetylation of histones play noteworthy roles in transcriptional regulation of eukaryotic cells *Address correspondence to this author at the SLT Institute of Pharmaceutical Sciences, Guru Ghasidas University, Bilaspur-495 009 (CG) India; Tel: +919827911824; E-mail: [email protected] 0929-8673/14 $58.00+.00

and are catalyzed by distinctive enzyme families: histone acetyl-transferases (HATs) and HDACs, respectively. These two kinds of enzymes play important role in the dynamic balance between acetylation and deacetylation of histone protein which results accurate regulation for gene transcription and gene expression of eukaryotes at DNA level. Unbalance of them can bring the disorder of proliferation and differentiation in normal cells and then lead to the initiation of tumor. HATs were initially identified as transcriptional coactivators and HDACs as yeast transcriptional regulators. Acetylation of the -NH2 group on lysine residues within histone tails correlates with nucleosome remodelling and transcriptional activation. Most of the identified human HATs function as transcriptional co-activators and are recruited to chromatin by interacting with sequence-specific DNA binding proteins. HDACs catalyse the removal of acetyl groups from lysine residues in histone amino termini, leading to chromatin condensation and transcriptional repression [4]. In this way, HDACs involve in the remodeling of chromatin and down-regulate many genes expression. The altered expression and mutations of genes that encode HDACs have been concomitant with tumor growth as they induce abnormal transcription of vital genes regulating imperative cellular functions such as cell proliferation, cell cy© 2014 Bentham Science Publishers

2 Current Medicinal Chemistry, 2014, Vol. 21, No. 1

cle regulation and apoptosis. In addition, deacetylation of nucleosomal histones play role in other genome functions, including chromatin assembly, DNA repair and recombination. This indicates that their aberrant functions are directly related to the initiation and progression of various tumors, so HDACs have been an important target enzyme in anticancer drug research [5]. Thus HDACi have emerged as a new class of chemotherapeutic drugs that regulate gene expression by increasing the acetylation of histones leading to induction of chromatin relaxation and alteration of gene expression (Fig. 1). The HDACs can be divided into two families- the Zn2+dependent HDAC and zinc independent HDAC. These two families comprise a family of 18 genes that are subdivided into four classes. Zn2+-dependent HDAC family composed of class I (HDACs 1, 2, 3 and 8), class II a/b (HDACs 4, 5, 6, 7, 9 and 10), and class IV (HDAC 11) and Zn2+-independent NAD-dependent class III SIRT enzymes. Out of these 18 HDACs in humans, 11 are zinc-dependent and fall into 4 classes on the basis of homology to yeast HDACs; the others are not zinc-dependent and not inhibited by compounds that inhibit zinc-dependent deacetylases [1, 6, 7]. Classes I and II comprise of 10 structurally related HDACs containing active zinc (Zn++) as a critical component of the enzymatic pocket. These HDACs are associated with cancers and are, potentially, inhibited by HDACi in the development [8]. All these HDACs are widely distributed in chromatin and the regulation of HDAC activity can occur at multiple levels including protein-protein interaction, post-translational modification and by metabolic co-factors. A rationale for structural design is derived from the Xray crystal structure of a bacterial HDAC homolog, Histone Deacetylase Like Protein (HDLP) with bound Trichostatin A (TSA). It has been suggested that the active site consists of a narrow tubular pocket with a zinc atom inside. Comparison of the amino acid sequences around the active site has indi-

Fig. (1). Role and mechanism of HAT, HDAC and HDACi.

Rajak et al.

cated that the structural features of the active site are well conserved across all the HDACs, with exceptions at the solvent-exposed rim of the pocket. Based on these studies, it has been rational that alteration of the spacer (linker) and surface recognition group, which are assumed to interact with the entrance area of the catalytic pocket, will provide prospects for discovering potent and possibly selective HDACi. In 2006, Suberoylanilide hydroxamic acid (SAHA also known as Vorinostat) became the first HDACi to receive FDA approval and was employed for the management of the cutaneous manifestations of T-cell lymphoma (CTCL). HDACi generally conform to a broadly accepted pharmacophore. The crystallographic studies for the design of valuable HDACi have pointed out three structural requirements- surface recognition moiety i.e., cap group (A) that provides interaction with the pocket entrance, a terminal group (B) that can bind to the zinc ion at the bottom of the active site, also known as zinc binding group (ZBG) and between both, a linker (C) fitting the tube-like portion of the binding pocket [9-11]. (Fig. 2) Several classes of HDACi have been identified including hydroxamic acid, benzamides, cyclic tetrapeptides, electrophilic ketones, short-chain fatty acids, benzofuranone- and sulfonamides- containg compounds, boronic acid-based compounds [12]. Out of all these classes, hydroxamic acid based HDACi constitute one of the major classes on which numerous studies has been reported and it continues to be an active area of research. Currently, lots of structurally diverse HDACi are in clinical trials either as monotherapy or in combination therapy for treatment of different hematologic and solid tumors. Several hydroxamic acid based HDACi i.e., vorinostat, panobinostat, belinostat, givinostat, PCI24781 and JNJ26481585 are in clinical trials. Vorinostat was the first of the HDACi to be approved for the treatment of CTCL by US FDA. It is also being evaluated in Phase II and III clinical trials as mono-

Hydroxamic Acid Based HDAC Inhibitors

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

3

Fig. (2). Presence of vital structural features in clinically tested hydroxamic acid based HDACi. A = cap group, B = linker, and C = zinc binding group.

therapy and in combination with other anticancer drugs including bortezomib, azacitidine, decitabine, proteasome inhibitors and taxanes [13]. Pantobinostat (LBH589) has been found more potent than vorinostat in preclinical studies [14]. It is in clinical trials for treatment of solid tumors in combination with DNA methylase inhibitors (azacitidine) and proteasome inhibitors. Other HDACi belonging to hydroxamic acid class i.e., belinostat, givinostat, PCI24781, and JNJ26481585 are also in clinical trials [15, 16]. Belinostat is in Phase I and II clinical trials for treatment of metastatic and refractory ovarian cancer. Givinostat is being investigated in a clinical trial in patients with pretreated refractory Hodgkin’s disease with oral administration [17, 18]. Besides vorinostat, there are more than 8 other HDAC inhibitors (Table 1) undergoing active clinical investigation. It is noteworthy that ITF2357 showed significant antiHodgkin lymphoma activity. Panobinostat showed consistent anti-leukemic effects. Belinostat appears to be promising for treating Low malignant potential ovarian tumor. The synergistic effects of HDACi in combination with other drugs may depend on the sequence of drug administration. These studies have guided, in part, clinical development of HDACi in combination therapeutic clinical trials. There are ongoing clinical trials with HDACi in combination therapy with radiation, cytotoxic agents and different targeted anticancer agents. These clinical trials include patients with cancer of lung, breast, pancreas, renal and bladder, melanoma,

glioblastoma, leukemias, lymphomas and multiple myeloma. Each of the hydroxamic acid-based HDACi in clinical trials has shown antitumor activity, including stable disease, partial response and in a few cases, complete responses of transient duration at doses generally well tolerated by the patients [19-24]. Table 1.

HDACi Under Clinical Trials [13-24]

S. No.

Drugs

Clinical Phases

1.

Vorinostat (SAHA)

Approved by US FDA

2.

Panobinostat (LBH589)

II & III

3.

Givinostat (ITF2357)

II

4.

Belinostat (PXD101)

I & II

5.

Abexinostat (PCI-24781)

I & II

6.

Quisinostat (JNJ-26481585)

I & II

7.

SB939

I & II

8.

CUDC-101

I

9.

Resminostat (4SC-201)

I

10.

CHR-2845 & CHR-2847

Preclinical Phase

4 Current Medicinal Chemistry, 2014, Vol. 21, No. 1

2. SYNTHETIC HYDROXAMIC ACID-CONTAINING HDACI The HDACi are being continuously designed and synthesized for their evaluation as anticancer agents. The present paper focuses specifically on hydroxamic acid based HDACi and a discussion of available literature. 2.1. Hydroxamic Acid Based HDACi Containing Aliphatic Spacers Histone deacetylase inhibitors containing aliphatic linker can be further divided into different subclasses on the basis of branching and saturation of alkyl chains. 2.1.1. HDACi Containing Saturated Straight Chain Aliphatic Spacer Generally all SAHA type hydroxamic acid based HDACi have common structural characteristics: zinc-binding group (ZBG) in the catalytic pocket, opposite capping group, and straight-chain alkyl, vinyl, or aryl linker connecting the two. These functional groups interact with three relatively conserved regions of the catalytic pocket of HDACs [22]. A novel series of chain-extended compounds (1) (Table 2), based on the amide linker template of HDACi, were designed and synthesized using computational and medicinal chemistry. The linker between the hydroxamic acid and amide must be at least five carbon atoms in length, with lengths of five and six being optimal. Introducing an alkyl spacer length of 2, 3, or 4 reduced both enzyme inhibitory and antiproliferative potency. This is due to the altered orientation of terminal aryl group of the inhibitors, which leads to a significant reduction in the biological activity [25]. In contrast to the alkyl spacer of SAHA and derivatives, insertion of the perfluorinated alkyl spacer (2) (Table 2) seems to facilitate the induction of selectivity for class II, particularly class IIa, HDACs [26]. Vaidya et al. studied about the HDAC inhibitors without a zinc-chelating hydroxamic acid moiety and suggested that the zinc-chelating moiety with hydroxamic acid group were more potent inhibitors than that of other zinc-chelating moieties such as methyl esters and t-Bu esters. The most potent ligand in the series (3) (Table 2) exhibits an IC50 of 28 M for HDAC8 [27]. Kozikowski et al. also considered the nature of the ZBG present in the HDACi to accomplish specific therapeutic endpoints. They compared the ability of HDACi containing either a hydroxamate or a mercaptoacetamide as the zinc binding group, and disclosed that some of the mercaptoacetamide-based HDACi are fully protective, whereas the hydroxamates (4,5) (Table 2) indicated toxicity at higher concentrations. The outcomes of these findings were consistent with the possibility that the mercaptoacetamide-based HDACi interact with an unlike subset of the HDAC isozymes or alternatively, interact selectively with only the cytoplasmic HDACs that are crucial for protection from oxidative stress [28]. Simple aryl systems like SAHA were generally well tolerated. Chen et al. reported results on the modification of the cap region of a set of triazolylphenyl-based HDACi (6) (Table 2) and showed that the nature of substitution on the phenyl ring played a role in their selectivity for HDAC1 ver-

Rajak et al.

sus HDAC6. The triazolyl ring incorporated with phenyl ring system showed the inhibition of HDAC6 (IC50 1.9 nM), this compound represented a valuable research tool and a candidate for further chemical modifications [29]. He et al. separately reported 1-aryl-1H-[1, 2, 3]triazolylphenyl-based analogs (7) (Table 2) and tested for their HDAC isoform selectivity and antiproliferative activities against pancreatic cell lines. One compound was found to be very effective inhibitor of cancer cell growth in vitro with the lowest IC50 value of 20 nM against MiaPaca-2 cell. It was found to reactivate the expression of CDK inhibitor proteins and to suppress pancreatic cancer cell growth in vivo [30]. The replacement of phenyl ring of SAHA with heterocyclic nucleus like benzothiazole produced active analogs (8) (Table 2) of SAHA. Oanh et al. observed that several compounds with 6C-bridge linking benzothiazole moiety and hydroxamic functional groups exhibited good inhibitory activity against HDAC3 and HDAC4 at as low as 1 g/ml and showed potent cytotoxicity against five cancer cell lines (SW620, MCF-7, PC3, AsPC-1 and NCI-H460) with average IC50 values of 0.81 g/ml, almost equipotent to SAHA [31]. A series of hydroxamic acid-based HDACi with an indole amide residue at the terminus was synthesized by Dai et al. Compounds (9) (Table 2) with a 2-indole amide moiety were found as the most active inhibitors among the different regioisomers. Introduction of a methyl group on the indole nitrogen caused a 3-fold decline in activity. This trend was also seen in the 3-indolyl analogs. However, the activity worsening was reversed when a benzyl group was introduced to the nitrogen atom. Introduction of substituents on the indole ring further enhanced the potency and produced a series of very potent inhibitors with noteworthy anticancer activity [32]. Removal of amide connecting unit from indole ring also produced active compounds. Giannini et al. designed and synthesized a series of hydroxamic acids containing a bis-(indolyl) methane moiety (10) (Table 2). They demonstrated that the bis-(indolyl) methane moiety can be used as a valid surface recognition cap in the design of HDACi. SAR analysis has concluded the relevance of the bis-(indolyl) methane moiety is more potent than the mono-indolyl analog (3-indolyl derivative is less potent than bis-(indolyl) analog) [33]. Tang et al. synthesized HDACi using building blocks having hydrazide, aldehyde and hydroxamic acid functionalities. The final compounds (11) (Table 2) were found to possess ‘cap/linker/biasing element’ features known to favour inhibition of HDACs HDAC8-selective inhibitors were discovered from this collection of compounds [34]. Salisbury and Cravatt (12) (Table 2) examined the impact of increasing the distance between the hydroxamate to the benzophenone for understanding the interplay between enzyme abundance and enzyme activity in living cells. They investigated the selectivity, sensitivity and inhibitory properties of SAHABPyne and related potential activity based probes for HDACs. Finally they demonstrated the value of in situ profiling of HDACs by comparing the activity and expression of HDAC1 in cancer cells treated with the cytotoxic agent parthenolide. These results underscore the utility of activity based protein profiling for studying HDAC function and may provide insight for the future development of click chemistry-based photoreactive probes for the in situ analysis of additional enzyme activities [35].

Hydroxamic Acid Based HDAC Inhibitors

Table 2.

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

HDACi Containing Saturated Straight Chain Aliphatic Spacer

Compound No.

Biological Activity (IC50)

Ref.

1

R

CONH

(CH2)n

0.4-113.5 μM

[25]

2

R

NHCO

(CF2) 6

8aminoquinolide > anilide was observed [52]. In order to see the effect of different connecting units, Wang et al. examined novel acylurea and sulfonylurea connecting unit attached with alkyl hydroxamates (30,31) (Table 2). The acylurea moiety has more hydrogen bond acceptors and donors as compared to amide or urea; hence orientation of the linker and cap group may change, thus influencing potency as well as isoform-selectivity. N-alkylated urea and acylurea connected straight chain hydroxamates showed much reduced HDAC potency due to unfavorable interactions at the binding pocket rim region. Bromine, phenyl, naphthalene and chloro aniline substituted cap groups showed 10–20-fold enhanced HDAC1 activity as compared to SAHA. Structure activity relationship (SAR) was estab-

Hydroxamic Acid Based HDAC Inhibitors

lished for the length of linear chain linker and substitutions on the benzolylurea group. They demonstrated that the bulkier linker shows more inhibitory activity towards HDAC. They illustrated that the bulkier linker can directly interact with the hydrophobic pocket of HDAC enzyme. In general, these compounds showed good stability (t1/2 >30 min) in human liver microsomal assay [53]. To see the effect of oxygen as connecting unit, a series of aryloxyalkanoic acid hydroxyamides (32-34) (Table 2) was synthesized for their HDAC inhibitory activity. Researchers incorporated oxygen atom between aromatic cap group and alkyl spacer. Some compounds were found to be more potent in vitro than trichostatin A (IC50 = 3 nM). The potencies of aryloxyalkanoic acid hydroxyamides indicated that neither an amide group (as present in trichostatin A and SAHA) nor a rigid (alkylene) chain is essential for low nanomolar HDAC enzyme inhibition [54, 55]. Marek et al. developed new potent hydroxamate-based HDAC inhibitors (35) (Table 2) with a novel alkoxyamide connecting unit linker region. They demonstrated that the insertion of alkoxyamide connecting unit linker region contributes to the selectivity. This may be due to a charge-assisted hydrogen bond between the alkoxyamide nitrogen and the carboxylate group/sulfur atom of surrounding amino acid or additional polarization of the NH bond due to the presence of the N-alkoxy moiety [56]. Chen et al. incorporated a 1, 2, 3-triazole ring (36) (Table 2) as a surface recognition cap group-linking connecting moiety in SAHA-like HDACi. Using ‘‘click’’ chemistry (Huisgen cyclo-addition reaction), several triazole-linked SAHA-like hydroxamates were synthesized. Docking analysis on histone deacetylase-like protein (HDLP) with respect to SAHA into HDLP revealed that these compounds have preferences for two different binding pockets at the protein surface. SAR studies indicated that triazole-linked hydroxamates displayed a cap group dependent preference for either five- or six-methylene spacer groups. They demonstrated that the triazole ring directly attached to the phenyl cap group was more potent than triazole ring is separated from the cap group by a methylene group. This result indicates that the triazole ring is indeed an active participant in the interaction of this class of compound with the HDAC active site [57]. In further studies on HDACi, Dai et al. synthesized a series of structurally novel and potent HDACi, in which a five-membered heteroaromatic ring connects the spacer to the hydrophobic group. These compounds (37) (Table 2) are significantly more potent than SAHA in the HDAC enzymatic assay and showed impressive anticancer activity against the growth of human HT1080 fibrosarcoma and human MDA435 breast carcinoma cell lines [58]. Bigioni et al. developed a new series of compounds which contains amide connecting unit in the ring system and alkyl linker was directly attached to the nitrogen of amide. They designed and synthesized a series of 5,11dihydrodibenzo[b,e]azepine-6-ones (38) (Table 2) alkylated on the amide nitrogen with an alkyl chain bearing an hydroxamic acids moiety at the end. They explored that the diphenyl methyl privileged fragment recognition motif as a new series of HDACi. The endocyclic ketone was tolerated, but was not beneficial to the binding affinity, since it caused a three-fold drop in the IC50. The effect on cell activity was more dramatic probably due to decreased permeability [59].

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

9

Novel Ugi products containing a zinc-chelating moiety was synthesized by Grolla et al. The key reaction in the synthesis of the proposed HDACi was Ugi reaction, which leads to the -aminoacylamides displaying as ester function. One of compounds (39) (Table 2) exhibited improved inhibitory potencies compared to SAHA, demonstrating that hindered lipophilic residues grafted on the peptide scaffold of the aminoacylamides can be favorable in the interaction with the enzyme. Most of the compounds possessing the hydroxamate moiety exhibited cytotoxic activity comparable to that of SAHA [60]. 2.1.2. HDACi Containing Saturated Branched Chain Aliphatic Spacer The failures in development of hydroxamate based HDACi may be attributed to lack of selectivity, toxicity or poor stability. Flipo et al. defined some structural rules to predict or improve plasma stability of hydroxamate based HDACi. They concluded that methylation of the  position to the electrophilic carbonyl group increases the stability. Plasma stability of hydroxamates seems to be the result of two opposing factors. Stabilizing factors are the steric hindrance around the hydroxamate group and the mesomeric effects that reduce the electrophilic nature of the carbonyl group. These results allowed the researchers to hypothesize a preliminary pharmacophore for plasma hydrolysis or stability of hydroxamic acids [61]. On the basis of this concept researchers modified Vorinostat (SAHA), a FDA-approved drug to improve its selectivity for a single HDAC isoform. It has been found that attaching an ethyl group at the C3 position transforms SAHA from nonselective to an HDAC6selective inhibitor. C3-ethyl analog (40) (Table 3) displayed 12-fold selectivity for HDAC6 over HDAC3 and three fold selectivity for HDAC6 over HDAC1. Thus, these studies indicate that isoform selective SAHA analogs can be generated by attaching a substituent to the linker chain. While the C3-methyl analog displayed potency comparable to SAHA (four fold reduced), and C2-methyl analog displayed 1488fold reduced activity versus SAHA. Interestingly, the C3-nbutyl variant is less potent than C2-n-butyl analog suggesting that the area of the HDAC active site near the C2 and C3 linker positions displays structural differences [62]. A dramatic reduction in potency (120-fold) was detected with the introduction of a 2-methyl group (41) (Table 3) adjacent to the hydroxamic acid moiety, whereas the 3-methylated derivative was less damaging to HDAC inhibition (6-fold less potent than compound without any substitutions at 3position) [40]. Two different series of naphthalene and anthracene based hydroxamic acid derivatives (42, 43) (Table 3) were synthesized by Chawdhary et al. They demonstrated that the single strand DNA cleavage was achieved by both reactive oxygen species (ROS) and generated radicals from hydroxamic acids. Further, DNA cleaving ability of hydroxamic acids was found to be dependent on its concentration and on its structure [63]. 2.1.3. HDACi Containing Unsaturated Straight Chain Aliphatic Spacer A series of compounds was investigated by varying the structure and unsaturation of linker chain between the termi-

10 Current Medicinal Chemistry, 2014, Vol. 21, No. 1

Table 3.

Rajak et al.

HDACi Containing Saturated Branched Chain Aliphatic Spacer

Biological Activity (IC50)

Ref.

NHCO

0.35- 184±14 μM

[62]

41

CO

0.6 μM

[40]

42

NH

_____

[63]

43

CONH

_____

[63]

Compound No.

40

Ph

nal hydroxamic acid and aryl cap group in order to obtain more stable and potent HDACi. The natural piperamide derivatives (44) (Table 4) were synthesized and evaluated for inhibitory activity against HDACs, as well as the HCT-116 human colon cancer cell line. Compounds with hydroxamic acid as their zinc-binding moiety exhibited moderate HDACs inhibitory activity while compounds with carboxylate acid and amides showed no inhibitory activity. Thus Luo et al. confirmed that hydroxamic acid is generally a more potent HDACi than carboxylate acid. Furthermore, they observed that analogs with longer spacer group (8 atom chain lengths, including linker and connecting unit) exhibited more potent inhibition compared to analogs with shorter spacer group with chain length of 4 or less atoms. They also reported that the insertion of unsaturated system adjacent to aromatic ring (inplace of amide linkage in SAHA) is more active than the unsaturation at longer distance. This may be possible due to sterically restricted double bond must have an influence on the shape of the molecule [64]. Marson et al. disclosed synthesis of a novel series of potent inhibitors of HDACi based on arylsulfinyl-2, 4-hexadienoic acid hydroxyamides and their derivatives (45, 46) (Table 4). Incorporation of sulfide or sulfoxide group in place of amide connecting group as part of an alkyl or an alkylene chain, with hydrophobic capping region, provide good potency and much greater metabolic stability than SAHA and TSA. Although in the enzyme assay, sulfoxides were generally more potent than the corresponding sulfides. In vitro IC50 values down to 40 nM were observed and several compounds exhibited inhibition of CEM (human leukemic) cell viability with IC50 value of around 1.5 μM, comparable to or better than that of SAHA [65]. 2.1.4. HDACi Containing Unsaturated Branched Chain Aliphatic Spacer In order to develop potentially superior HDAC inhibitors based on TSA or SAHA Pabba et al. reported TSA analogs

(47) (Table 5) containing either an aryl ether or sulfone functionality as connecting unit with the capping group, a branched chain diene linker and carboxylic or hydroxamic acid terminal group capable of binding to the zinc residue contained within the active site of HDAC enzyme. They observed manifold increase in HDAC inhibitory activity with the replacement of large arylsulfone group with the corresponding aryl ether [66]. The introduction of the (R)-methyl group and of the diene function, which are present in TSA, into the amide bond analogs does not result in an increased HDAC inhibitory potency. [39]. Charrier et al. reported synthesis of novel benzofuranones (49) (Table 5) and evaluated them against NCI-H661 non-small cell lung cancer cells. They demonstrated that the benzofuranone cap region does not have a preferred orientation typical for hydrophobic interactions [67]. 2.2. Hydroxamic Acid Based HDACi Containing Cyclic Spacers 2.2.1. HDACi Containing Phenyl Ring Cyclic Spacers A novel series of HDACi possessing sulphonamide group as connection unit and aromatic spacer (50-54) (Table 6) exhibited promising activity in HDAC inhibitory assay and antiproliferative activity. These compounds were characterized by a cinnamic spacer, capped with a substituted phenyl group. Most compounds showed an antiproliferative activity comparable to that of SAHA. At equitoxic concentrations, the tested compounds were more effective than SAHA in inducing apoptotic cell death. The 4-phenyl-cinnamic acid scaffold was found essential for a good cytotoxic activity on different cell lines. Modification of the position of the side chain, or replacement of the proximal ring with a cyclohexyl led to substantial decrease in the activity. Further optimization of this series by substitution of the terminal aromatic ring yielded HDACi with good in vitro and in vivo activities. N-Methylation of sulphonamide decreased the activity. For HDAC inhibitory activity, the optimal chain length between

Hydroxamic Acid Based HDAC Inhibitors

Table 4.

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

HDACi Containing Unsaturated Straight Chain Aliphatic Spacer

Compound No.

Biological Activity (IC50)

Ref.

44

________

1.61±0.17 μM (HDAC1) 2.25±0.30 μM (HDAC6) 1.52±0.13 μM (HDAC3) 3.5±0.4 μM (HCT116)

[64]

45

SO

0.24±0.03 μM

[65]

46

________

> 25 μM

[65]

Biological Activity (IC50)

Ref.

O / SO2

0.018- 1.2 M

[66]

48

CONH

152±15 nM

[39]

49

______

45 nM

[67]

Biological Activity (IC50)

Ref.

Table 5.

HDACi Containing Unsaturated Branched Chain Aliphatic Spacer

Compound No.

Ar

47

Table 6.

HDACi Containing Phenyl Ring Cyclic Spacers

Compound No.

50

SO2NH

____

[68]

51

SO2NH

0.075-0.2 μM

[69]

SO2NH

____

[69]

53

SO2NH

50 nM

[70]

54

SO2NH

____

[71]

SO2NH/ NHSO 2/ NHCONH

0.01- 0.5 μM

[72]

_________

0.32±0.024 μM

[73]

52

55

56

Ar

Ar

11

12 Current Medicinal Chemistry, 2014, Vol. 21, No. 1

Rajak et al.

(Table 6) contd….

CONH

172.02±8.22 nM

[74]

58

S/ SO2

0.16±0.82μM

[65]

59

_________

1.82 μM (HDAC2) 0.11 μM (HDAC6) 1.21 μM (HDAC8)

[75]

60

_________

1.3-49 nM

[43, 76]

0.55±0.14 μM

[77]

57

R

61

62

NHCO

6 nM

[78]

63

CONH

10-20 μM

[79]

64

S

34±1.7 nM (HDAC1)

[80]

65

CO

0.057- 0.34 μM

[81]

O

3.6±0.2- 82.5±9.3μM

[82]

66

R1

the aryl and the hydroxamate was found to be two carbons. These studies confirmed that steric bulk is not tolerable near the zinc binding site. It was observed that double bond analogs possess more than a 10-fold enhanced potency compared with the triple bond analog oxamflatin (Fig. 2). The ecacy of arylpenta-2, 4-dienoic acid hydroxyamides shows that neither the keto group nor the full seven-carbon chain in trichostatin A is vital for potent enzyme inhibition. They also confirmed that trans, trans-stereochemical rigidity is desirable, presumably providing a locking of conformation similar to that conferred by the trans, trans-configuration and zigzag backbone of trichostatin A. Incorporation of a 4-methyl group in unsaturated chain present between ZBG and phenyl linker increased in vitro potency over two orders of magnitude; a remarkable observation that it has comparable potency with trichostatin A. Substitution on p-position of cap group with chloro group analog showed a greater potency for HDAC inhibition and MTT assay than the 3,4-dichloro and 2,4-dichloro derivatives. A more electron withdrawing group present in p-position seems to be deleterious for potency [6871]. The replacement of the sulfonamide function with the urea resulted in decreased enzymatic activity and is detri-

mental for histone acetylation. All hydroxamates were more potent as HDACi as compared to the corresponding carboxylic acids, probably due to the increased Zn (II) coordinating properties of the hydroxamate moiety. In the hydroxamic series, compounds exhibited potent antiproliferative activity against human cancer cells with IC50 values from 0.024 to 2 μM. No difference was seen between the sulfonamide and the “reverse” sulfonamide derivatives during anticancer activity [72, 73]. Kim et al. disclosed 3-(4-substituted-phenyl)-N-hydroxy2-propenamides (57) (Table 6) as a novel class of HDACi and evaluated for their antiproliferative activity and HDAC inhibitory activity. Incorporation of a 1,4-phenylene carboxamide linker and a 4-(dimethylamino) phenyl or 4(pyrrolidin-1-yl) phenyl group as a cap substructure produced highly potent hydroxamic acid-based HDACi. This was found to induce cell cycle arrest at G1 and G2/M phases and mitochondrial- and caspase-dependent apoptotic cell death. Marson et al. suggested that a sulfide or a sulfoxide linkage (58) (Table 6) as connecting unit attached with an alkyl/alkylene chain aryl linker, together with an extended hydrophobic capping region, could provide good potency

Hydroxamic Acid Based HDAC Inhibitors

and good antiproliferative properties with comparable or better metabolic stability than SAHA and much greater metabolic stability than TSA [65, 74]. In order to find potent, antiproliferative HDACi, several series of hydroxamic acids derivatives with different combination of substituted cap groups like uracil, phenyl/phenyl alkyl, valproate, phenylbutyrate, indole, arylindole, arylbenzofuran, L-tyrosin and connecting units along with cinnamyl linker based hydroxamates (59-66) (Table 6) were reported. Some of the hydroxamate compounds were almost equal in potency to the positive control SAHA [43, 75-82]. 2.2.2. HDACi Containing Six Member Non-aromatic & Heterocyclic Spacers To improve metabolic stability of HDACi, nonaromatic hetrocyclic linker -lactam analogs (67) (Table 7) were prepared and evaluated on their HDAC and cancer cell growth inhibitory activities using PC-3 (Prostate cancer), MDA-MB231 (breast cancer), ACHN (renal cancer), NUGC-3 (gastric cancer), HCT-115 (colon cancer) and NCI-H23 (lung cancer) cell lines. Most of meta- or para-substituted aromatic cap group analogs were active and relatively bulky groups were more active than smaller substituents. The microsomal stability assay was performed to evaluate effect of substituents on the cap group. Highly lipophilic compounds showed high metabolic clearance. Higher number of rotatable bonds resulted in the negative impact on microsomal stability by increasing lipophilicity. These analogs also showed a good HDAC enzyme inhibitory activities and cancer cell growth inhibitory activities [83]. The potencies of these -lactam analogs were also related to the chain length between the cap group and the zinc binder group. Incorporation of 3-4 carbon units between the cap group and the -lactam ring, and two carbon units between the -lactam ring and the zinc binder group, were essential for optimal for potency which was also confirmed by docking studies [84]. Insertion of phenyl, naphthyl and thiophenyl cap group increases potency of HDAC inhibition because of better hydrophobic interaction between HDAC and inhibitors. 4-methoxy substituted analogs with one carbon atom spacer between cap and -lactam ring were more active than methyl analogs in the HDAC enzyme assay. 4-Fluoro and 4-bromo analog showed the same range of activities to 4-methoxy analog but 4-nitro analog exhibited better inhibitory activities. Surprisingly, 2naphthyl analog did not show any activity while its chain elongated analogs (n = 2, n = 3) showed very strong inhibitory activity at 37 and 30 nM of IC50, respectively. 1Naphthyl analogs were less active than 2-naphthyl analogs. 4-N-Acyl and sulfonylated aryl analogs showed moderate inhibitory activities ranging from 0.5 to 0.8 μM of IC50. Among these prepared analogs, 2-naphthyl analogs were the best compounds in HDAC inhibitory assay. -Lactam based HDACi exhibited better activity than -lactam analogs. The smaller core was suggested as more active than larger one because -lactam core has reduced ring size and results in better binding in narrow hydrophobic tunnel of the active pocket of HDAC enzyme [85, 86]. A series of N-substituted 4-alkylpiperazine and 4alkylpiperidine hydroxamic acids, corresponding to the basic structure of HDACi (zinc binding moiety-linker-capping group) were designed synthesized and evaluated for HDAC

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

13

inhibition by Rossi et al. The compounds (71, 72) (Table 7) were characterized by having a 4-propylpiperidine as the linker, a hydroxamic acid as the zinc binding moiety and can tolerate a phenyl ring linked through a sulfonamide, an urea and an amide with or without a methylene as an additional spacer. The variation of linker length and aromatic cap resulted in identification of submicromolar inhibitors possessed antiproliferative activity on HCT-116 colon carcinoma cells. The results obtained were indicating that the 3 carbon atom spacer was optimal for activity. Results also indicated that the binding of piperazine linker with enzyme was very poor. This was due to its basic character, which requires a desolvation energy gap to be overcome prior to entering the hydrophobic tunnel [87]. Chetan et al. also synthesized piperazine linker based HDACi (73) (Table 8) and screened for their anticancer activity against HL60 human promyelocytic leukemia cell lines. Due to the presence of pharmacophoric features of ribonucleotide reductase inhibitors promising results were obtained in biological evaluations [88]. Recently, our research group has reported two novel series of 2-5-(4-substitutedphenyl)-1,3,4.-oxadiazol/thiadiazol2-ylamino.-pyrimidine-5-carboxylic acid (tetra hydro-pyran2-yloxy)-amides (74) (Table 7) as novel hydroxamic acid based HDACi. The antitumor activity of test compounds was found to vary on changing para-substituted group of aryl moiety attached to 1,3,4-oxadiazole/thiadiazole in the order as follows, hydroxy > methoxy > methyl > amino > dimethylamino > nitro > chloro > fluoro > no substitution. It was noted that para-chloro analogs showed greater potency than parent compound in HDAC inhibition and MTT assay. The position of the substitution had dramatic effects on the HDAC activity. Ortho- and meta-substituted analogs were found to be lesser active than para-substituted analogs. Overview of results indicated that thiadiazole analogs were more activity than corresponding oxadiazole analogs [89]. Dallavalle et al. designed and synthesized a new class of hydroxamic acid HDAC inhibitors. They demonstrated that 4-phenylcinnamic scaffold (75) (Table 7) required for a good cytotoxic activity on different cell lines. Modification in position of the side chain, or replacement of the proximal ring with a cyclohexyl, led to substantial decrease of the activity. The length and type of the chain tolerated some changes. The unsaturation in the side chain situated between cyclic linker and ZBG, made the ligand more active. On the contrary, reduction of the double bond in the chain, which imparted additional flexibility to the spacer, was not beneficial. These results indicated the importance of the double bond adjacent to the hydroxamic group. A variety of substitutions in the distal ring were also well tolerated [73]. A series of N-hydroxycarboxamides (76) (Table 7) were synthesized using tranexamic acid as a starting material to develop novel HDACi. The structure optimization involved the replacement of 1,4-cyclohexylene group with the 1,4phenylene group resulted in the promising HDACi possessing a terminal bicyclic aryl amide [90]. 2.2.3. HDACi Containing Five Member Cyclic Spacers Choi et al. and Lee et al. separately designed and synthesized five membered -lactam core HDACi (77, 78)

14 Current Medicinal Chemistry, 2014, Vol. 21, No. 1

Table 7.

Rajak et al.

HDACi Containing Six Member Non-aromatic and Heterocyclic Spacers

Compound No.

67

R

_______

H2C CH 2

Biological Activity (IC50)

Ref.

0.01- 0.80 μM

[83, 86]

0.50 μM

[84]

68

_______

69

______

0.51 μM

[85]

70

______

0.030 μM

[85]

71

R R = Ph, PhCH2

X X = CO; SO2

0.09- 1.39 μM

[87]

72

R

X

0.09-1.30 μM

[87]

73

Ar

9.33±1.3 μM

[88]

74

________

0.006- 0.018 μM

[89]

75

________

0.31±0.003 μM

[73]

CONH

9.4 μM

[90]

Biological Activity (IC50)

Ref.

0.01- 0.80 μM

[86]

_______

0.07- >10 μM

[91]

CONH

17.7 μM (HDAC1) 36.2 μM (HDAC2) 28.1 μM (HDAC3) 0.76 μM (HDAC6) 23.9 μM (HDAC10)

[92]

Ar

76

Table 8.

HDACi Containing Five Member Cyclic Spacers

Compound No.

77

R

78

79

Ph

Hydroxamic Acid Based HDAC Inhibitors

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

15

(Table 8) contd….

Compound No.

Biological Activity (IC50)

Ref.

80

R

NHCO

139±4 nM (HDAC1) 164±4 nM (HDAC2) 25±1 nM (HDAC3) 82±5 nM (HDAC6) 250±6 nM (HDAC10)

[93]

81

Ar

CO

3.77 μM (HDAC1) 4.38 μM (HDAC4)

[94]

________

0.019 μM

[95]

________

0.186 μM

[96]

0.004- 0.581 μM

[96]

CO

4.2±4 μM

[97]

82

83

Ar

84

85

86

R

CO

0.043±0.003 μM

[98]

87

R

CO

0.20±0.006 μM

[99]

CO

0.78±0.04 μM

[100]

__________

____

[101, 102]

__________

18- 838 nM

[103]

88

89

90

R

(Table 8) for biological and property optimization. The lactam core has reduced ring size and resulted in better binding in narrow tunnel of active site. The phenyl, naphthyl and thiophenyl groups were employed as the cap groups. The hydrophobic and bulky cap groups increased the potency of HDAC inhibition because of better hydrophobic interaction between HDAC and inhibitors. The HDACi with diverse carbon chain linker and various substituents on cap groups were prepared to improve HDAC inhibition profiles. They

prepared 1-3 carbon chain linker between -lactam core and cap group with methoxy, trifluoromethyl substituents of ortho-, meta-, para-positions of cap groups. These modifications of analogs led to better potency, while the metabolic stability slightly decreased. The analogs with 2-carbon chain linker and trifluoromethyl substituents showed the best HDAC inhibitory activity, because 2-carbon chain linker provided proper fitting into active site of HDAC and trifluoromethyl substituents on cap group increased lipophil-

16 Current Medicinal Chemistry, 2014, Vol. 21, No. 1

icity. Larger lipophilicity of the analogs increased hydrophobic interaction between surface of HDAC active site and HDAC inhibitor and produced better HDAC inhibitory activity [86, 91]. A series of isoxazole-based HDACi (79, 80) (Table 8) structurally related to SAHA was designed and synthesized. The isoxazole moiety was inserted in the vicinity of the Zn2+binding group in order to check its participation in the coordination process. The replacement of the hydroxamate group by the other functional groups such as alcohol, carboxylic acid and amide, failed to provide any significant HDAC inhibitory activity. Some of these compounds exhibited nanomolar activity in the HDAC isoform inhibitory assay and exhibited micromolar inhibitory activity against pancreatic cancer cell lines. These studies concluded that insertion of an isoxazole or isoxazoline ring into the SAHA skeleton did not significantly modify the selectivity profile towards different HDAC isoforms [92, 93]. Su et al. reported a series of hydroxamic acids with stereo-defined conjugated structures. Some analogs (81) (Table 9) showed significant effect on arresting cell cycle progression. The selectivity as well as the inhibitory potency of these compounds against mammalian HDAC1 and HDAC4 was found limited. Some of these compounds exhibited significant effect in inducing apoptosis. The anticancer activity in cancer cells was found promising especially with HCT119 cell lines [94]. With the optimization of ADS100380, a sub-micromolar HDACi identified using a virtual screening approach, led to a series of substituted 5-(1H-pyrazol-3-yl)-thiophene-2hydroxamic acids (82-84) (Table 8) that possessed significant HDAC inhibitory activity (Fig. 3). Subsequent functionalization of the pendent phenyl group of compounds provided analogs with further improved enzyme inhibition and anti-proliferative activity. The benzyl-tethered compound possessed a 5-fold increase in HDAC potency over ADS100380, both in the HDAC and the MCF-7 cell proliferation assays. Replacement of the pyrazole ring of ADS100380 with a thienyl ring resulted in 4-fold reduction in activity in the HDAC enzyme assay and a 10-fold reduction in the MCF-7 cell-based assay (Fig. 3). These compounds demonstrated improve cytochrome P450 3A4 inhibition, Caco-2 permeability and increased oral bioavailability in rat, compared to ADS102550. Increasing the linker length by a methylene group resulted in minor increase in HDAC inhibitory activity, whereas increasing the linker length by two methylene units resulted in more than 4-fold increase in HDAC inhibitory activity [95, 96]. Mai et al. reported the binding mode of HDACi i.e., 3-(4aroyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamides (85) (Table 8), into the new modelled HDAC1 catalytic core. The most potent compound displayed antiproliferative (45 and 85% cell growth inhibition at 40 and 80 μM concentration) and cellular differentiation (18 and 21% of benzidine positive cell at 40 and 80 μM concentration) activities in murine erythroleukemic cells. The most active derivative (IC50 1.9 μM) showed a 500-fold higher inhibitory potency than NaB and a 264-, 38-, 190- and 17-fold lower potency than TSA, SAHA, TPX and HC toxin, respectively [97]. They also explored the effect on anti-HDAC2 activity of chemical substi-

Rajak et al.

tutions performed on the pyrrole-C2 ethene chains of compounds (86) (Table 8) which were replaced with methylene, ethylene, substituted ethene and 1, 3-butadiene chains. Biological data clearly showed the unsubstituted ethene chain is best structural motif to achieve the maximum HDAC inhibitory activity. IC50 values of compounds revealed that between benzene and carbonyl groups at the pyrrole-C4 position a hydrocarbon spacer length ranging from two to five methylenes was well accepted by the aroyl-pyrrolylhydroxyamide (APHA) template. The introduction of a higher number of methylene units reduced the inhibitory activities of the derivatives. APHA derivatives showed significant antiproliferative and cyto-differentiating activities in vivo on Friends MEL cells [98]. They also disclosed chemical manipulations performed on aroyl-pyrrolylhydroxyamides (APHAs) (87) (Table 8) resulted in development of (aryloxo-propenyl)pyrrolyl hydroxamates and their inhibition against maize HDACs and their class I or class II HDAC selectivity. From these studies some benzene m-substituted compounds emerged as highly class II (IIa)selective HDACi, the most selective being the 3-chloro- and 3-fluoro-substituted compounds. The replacement of benzene with a 1-naphthyl ring afforded compound with high activity against the class II homolog HDAC1-A (IC50 10 nM). 1-naphthyl analogs were found to have 2-fold lesser potent than SAHA [99]. Ragno et al. designed, synthesized and evaluated two new isomers (88) (Table 8) of APHA lead compound 3-(4-benzoyl-1-methyl-1H-pyrrol-2-yl)-Nhydroxy-2-propenamide (A) compound (C) and (D) (Fig. 3), characterized by different insertions of benzoyl and propenoylhydroxamate groups onto the pyrrole ring. In particular, in mouse HDAC1 inhibitory assay (C) and (D) were 19- and 6-times more potent than (A) and (C) and (D) antimaize HDAC2 activities were 16- and 76-times higher than that of (A) and (D) being as potent as SAHA in this assay [100]. All compounds which differ essentially by the nature of the pyrrole substituent displayed HDAC inhibitory activities in the micromolar to nanomolar range, the compound with a pmethyl group being more potent. Saturation of the double bond led to a decrease in the inhibitory potency [101, 102]. Hou et al. synthesized a novel series of cinnamyl derivatives (90) (Table 8) using click chemistry approach and observed that these derivatives possess potent HDAC inhibitory activity. The incorporation of isopropyl and tert-butyl group adjacent to triazole nucleus exhibited excellent potency against HDACs enzyme with an IC50 value of 22 nM and 18 nM, respectively. Incorporation of shorter-chain groups, such as methyl and ethyl increased potency, whereas straight chain groups larger than ethyl lead to a decrease in potency. Branching of alkyl chain resulted 5-fold increase in the potency compared to NSC746457. Incorporation of aromatic group resulted in some loss of potency, whereas the benzyl group was observed to slightly improve the potency [103]. 2.2.4. HDACi Containing Other Cyclic Spacers In order to obtain more selective and potent HDACi than SAHA, 2-aroylindoles (91) (Table 9) and 2-aroylbenzofurans with the hydroxamate head group were constituted as a new class of potent HDAC class I/II inhibitors. They found that the indole ring as a linker with an E-N-hydroxyacrylamide motif leads to compounds with a concentration-dependent

Hydroxamic Acid Based HDAC Inhibitors

Table 9.

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

HDACi Containing Other Cyclic Spacers

Compound No.

Biological Activity (IC50)

Ref.

91

CO

0.09- 0.34 μM

[81]

92

SO2

6.8±1.7 nM

[104]

93

________

92±6 nM (HDAC1) 56±7 nM (HDAC4) 280±10 nM (HDAC6)

[105]

________

0.08±0.04- 3.2 μM (HDAC1) 0.10±0.03 μM (HCT116)

[106]

________

572 nM (HDAC1) 358 nM (HDAC4) 709 nM (HDAC6)

[107]

96

CONH

___

[93]

97

NHCO

0.759±0.12 μM

[108]

94

95

17

R2

R

98

R1

X

___

[109]

99

Ar

X

0.070 μM

[110]

100

Ph

SO2NH

7 > 5 > 4. Studies also reveal that the saturated straight chain linker derivatives were more active than unsaturated linkers. A dramatic reduction in potency was detected with the introduction of an -methyl group adjacent to the hydroxamic acid moiety, whereas the -methylated derivative was less damaging to HDAC inhibition and more selective towards HDACs. The replacement of saturated chain with unsaturated chain between cyclic linker and hydroxamic acid group results in more potent analogs. At the same point, branching in unsaturated system causes reduction of activity. Insertion of rigid ring system adjacent to hydroxamic acid moiety leads to decreased activity. In case of connecting unit, amide linkage in SAHA is not critical for activity. Replacement of amide linkage with oxygen, sulfur, carbonyl, thiourea, methylene groups produces active compounds. Similarly, insertion of heterocyclic ring system as connecting unit also produces active derivatives (Fig. 4). Surface recognition moiety present around the catalytic site opening is normally a hydrophobic structure which interacts with the rim amino acids. The amino acid sequence of the circumference surrounding the catalytic site of the different HDACs has greater sequence diversity compared to the other domains and has most potential to be manipulated to generate selective HDACi. Various heterocyclic rings have been evaluated as surface recognition moiety and most of them have already been described in this review. There is a great deal of enthusiasm in the design and development of HDACi and increasing number of these compounds are in or entering clinical trials. The hydroxamic based HDACi have shown potential activity in preclinical studies and they may be considered as a promising class of therapeutic agents to develop more safer and effective anti-

Hydroxamic Acid Based HDAC Inhibitors

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

19

Fig. (4). Structure activity relationship of hydroxamic acid based HDACi.

cancer drugs. In the future, it might be possible to develop more effective HDACi from a better combination of cap group, connecting unit, linker and ZBG using information discussed herewith. The structure activity relationship among reported HDACi might also be helpful in the development of more isoenzyme-subtype-selective inhibitors infuture. It can be expected that these scientific endeavours in the area of HDACi research will provide fruitful results in the future.

HATs

=

Histone acetyltransferases

HDACs

=

Histone deacetylases

NF-YA

=

Nuclear factor-YA

GATA-1

=

Globin transcription factor-1

Rpd3

=

Reduced potassium dependency-3

Sirtuins or Sir2

=

Silent information regulators-2

CONFLICT OF INTEREST

ZBG

=

Zinc binding group

The author(s) confirm that this article content has no conflicts of interest.

HDLP

=

Histone deacetylase-like protein

TGF-beta

=

Transforming growth factor beta

ACKNOWLEDGEMENTS

REFERENCES

One of the authors, Avineesh Singh is thankful to CSIR, New Delhi, India for awarding Senior Research Fellowship and Kamlesh Raghuvanshi is thankful to AICTE, New Delhi, India for awarding Junior Research Fellowship and financial assistance. One of the authors, Harish Rajak is grateful to AICTE, New Delhi, India for awarding Research Project on anticancer evaluation of histone deacetylase inhibitors under Research Promotion Scheme.

[1]

ABBREVIATIONS

[2] [3] [4]

[5]

SAHA

=

Suberanilide hydroxamic acid

CTCL

=

Cutaneous T-cell Lymphoma

TSA

=

Trichostatin A

FDA

=

Food and drug administration

[7]

IC

=

Inhibitory concentration

[8]

GI

=

Growth inhibitory concentration

[9]

HDACi

=

Histone deacetylase inhibitors

[10]

DNA

=

Deoxyribonucleic acid

RNA

=

Ribonucleic acid

[6]

Venugopal, B.; Evans, T.R.J. Developing histone deacetylase inhibitors as anti-cancer therapeutics. Curr. Med. Chem., 2011, 18, 1658-1671. Acharya, M.L.; Sparreboom, A.; Venitz, J.; Figg, W.D. Rational development of histone deacetylase inhibitors as anticancer agents: a review. Mol. Pharmacol., 2005, 68, 917-932. Marks, P.A.; Miller, T.; Richon, V.M. Histone deacetylases. Curr. Opin. Pharmacol., 2003, 3, 344-351. Rajak, H.; Singh, A.; Dewangan, P.K.; Patel, V.; Jain, D.K.; Tiwari, S.K.; Veerasamy, R.; Sharma, P.C. Peptide based macrocycles: Selective histone deacetylase inhibitors with antiproliferative activity. Curr. Med. Chem., 2013, In press, PMID: 23409715. Ropero, S.; Esteller, M. The role of histone deacetylases (HDACs) in human cancer. Mol. Oncol., 2007, 1, 19-25. Martinez-Iglesias, O.; Ruiz-Llorente, L.; Sanchez-Martinez, R.; Garcia, L.; Zambrano, A.; Aranda, A. Histone deacetylase inhibitors: mechanism of action and therapeutic use in cancer. Clin Transl Oncol, 2008, 10, 395-398. Marks, P.A.; Xu, W.S. Histone deacetylase inhibitors: potential in cancer therapy. J. Cell. Biochem., 2009, 107, 600-608. Monneret, C. Histone deacetylase inhibitors. Eur. J. Med. Chem., 2005, 40, 1-13. Hess-Stumpp, H. Histone deacetylase inhibitors and cancer, from cell biology to the clinic. Eur. J. Cell Biol., 2005, 84, 109-121. Finnin, M.S.; Donigian, J.R.; Cohen, A.; Richon, V.M.; Rifkind, R.A.; Marks, P.A.; Breslow, R.; Pavletich, N.P. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature, 1999, 401, 188-193.

20 Current Medicinal Chemistry, 2014, Vol. 21, No. 1 [11] [12] [13] [14] [15] [16] [17] [18]

[19]

[20] [21] [22] [23] [24] [25]

[26]

[27]

[28]

[29]

[30]

[31]

[32]

Miller, T.A.; Witter, D.J.; Belvedere, S.J. Histone deacetylase inhibitors. J. Med. Chem., 2003, 46, 5097-5116. Prebet, T.; Vey, N. Vorinostat in acute myeloid leukemia and myelodysplastic syndromes. Expert Opin. Investig. Drugs, 2011, 20, 287-295. Wang, H.; Dymock, B.W. New patented histone deacetylase Inhibitors. Expert Opin. Ther. Patents, 2009, 19, 1727-1757. Zhang, L.; Fang, H.; Xu, W. Strategies in developing promising histone deacetylase inhibitors. Med. Res. Rev., 2010, 30, 585-602. Balasubramanian, S.; Verner, E.; Buggy, J.J. Isoform specific histone deacetylase inhibitors: The next step. Cancer Lett., 2009, 280, 211-221. Dokmanovic, M.; Clarke, C.; Marks, P.A. Histone deacetylase inhibitors: overview and perspectives. Mol. Cancer Res., 2007, 5, 981-989. Haberland, M.; Montgomery, R.L.; Olson, E.N. The many roles of histone deacetylases in development and physiology, implications for disease and therapy. Nat. Rev. Genet., 2009, 10, 32-42. Ramalingam, S.S.; Belani, C.P.; Ruel, C.; Frankel, P.; Gitlitz, B.; koczywas, M.; Espinoza-Delgado, I.; Gandara, D. Phase II study of belinostat (PXD101), a histone deacetylase inhibitors, for second line therapy of advanced malignant pleural mesothelioma. J. Thorac. Oncol., 2009, 4, 97-101. Golay, J.; Cuppinni, L.; Leoni, F.; Mico, C.; Barbui, V.; Domenghini, M.; Lombardi, L.; Neri, A.; Barbui, A.M.; Salvi, A.; Pozzi, P.; Porro, G.; Pagani, P.; Fossati, G.; Mascagni, P.; Introna, M.; Rambaldi, A. The histone deacetylase inhibitor ITF2357 has antileukemic activity in vitro and in vivo and inhibits IL-6 and VEGF production by stromal cells. Leukemia 2007, 21, 1892-1900. Kramer, O.H.; Gottlicher, M.; Heinzel, T. Histone deacetylase as a therapeutic target. Trends in Endocrin. Metabol. 2001, 12, 294-300. Ma, X.; Ezzeldin, H.H.; Diasion, R.B. Histone deacetylase inhibitors, current status and overview of recent clinical trials. Drugs, 2009, 69, 1911-1934. Marks, P.A. Histone deacetylase inhibitors as targeted anticancer drugs. Expert Opin. Investig. Drugs, 2010, 19, 1049-1066. Tan, J.; Cang, S.; Ma, Y.; Petrillo, R.L.; Liu, D. Novel histone deacetylase inhibitors in clinical trials as anti-cancer agents. J. Hematol. Oncol., 2010, 3, 1-13. Takai, N.; Kira, N.; Ishii, T.; Nishida, M.; Nasu, K.; Narahara, H. Novel chemotherapy using histone deacetylase inhibitors in cervical cancer. Asian Pacific J. Cancer Prev., 2011, 12, 575-580. Andrianov, V.; Gailite, V.; Lola, D.; Loza, E.; Semenikhina, V.; Kalvinsh, I.; Finn, P.; Petersen, K.D.; Ritchie, J.W.A.; Khan, N.; Tumber, A.; Collins, L.S.; Vadlamudi, S.M.; Bjo¨rkling, F.; Sehested, M. Eur. J. Med. Chem. 2009, 44, 1067-1085. Henkes, L.M.; Haus, P.; Jager, F.; Ludwig, J.; Meyer-Almes, F.J. Synthesis and biochemical analysis of 2,2,3,3,4,4,5,5,6,6,7,7dodecafluoro-N-hydroxy-octanediamides as inhibitors of human histone deacetylases. Bioorg. Med. Chem., 2012, 20, 985-995. Vaidya, A.S.; Neelarapu, R.; Madriaga, A.; Bai, H.; Mendonca, E.; Abdelkarim, H.; Van Breemen, R.B.; Blond, S.Y.; Petukhov, P.A. Novel histone deacetylase 8 ligands without a zinc chelating group: Exploring an ‘upside-down’ binding pose. Bioorg. Med. Chem. Lett., 2012, 22, 6621-6627. Kozikowski, A.P.; Chen, Y.; Gaysin, A.; Chen, B.; D’Annibale, M.A.; Suto, C.M.; Langley, B.C. Functional differences in epigenetic modulators superiority of mercaptoacetamide-based histone deacetylase inhibitors relative to hydroxamates in cortical neuron neuroprotection studies. J. Med. Chem., 2007, 50, 3054-3061. Chen, Y.; Sanchez, M.L.; Savoy, D.N.; Billadeau, D.D.; Dow, G.S.; Kozikowski, A.P. A series of potent and selective.; triazolylphenyl-based histone deacetylases inhibitors with activity against pancreatic cancer cells and plasmodium falciparum. J. Med. Chem., 2008, 51, 3437-3448. He, R.; Chen, Y.; Chen, Y.; Ougolkov, A.V.; Zhang, J.S.; Savoy, D.N.; Billadeau, D.D.; Kozikowski, A.P. Synthesis and biological evaluation of triazol-4-ylphenyl-bearing histone deacetylase inhibitors as anticancer agents. J. Med. Chem., 2010, 53, 1347-1356. Oanh, D.T.K.; Hai, H.V.; Park, S.H.; Kim, H.J.; Han, B.W.; Kim, H.S.; Hong, J.T.; Han, S.B.; Hue, V.T.M.; Nam, N.H. Benzothiazole-containing hydroxamic acids as histone deacetylase inhibitors and antitumor agents. Bioorg. Med. Chem. Lett., 2011, 21, 75097512. Dai, Y.; Guo, Y.; Guo, J.; Pease, L.J.; Li, J.; Marcotte, P.A.; Glaser, KB.; Tapang, P.; Albert, D.H.; Richardson, P.L.; Davidsen,

Rajak et al.

[33]

[34] [35] [36]

[37]

[38]

[39]

[40] [41]

[42] [43] [44]

[45]

[46]

[47]

[48]

[49]

[50]

S.K.; Michaelides, M.R. Indole Amide Hydroxamic Acids as Potent Inhibitors of Histone Deacetylases. Bioorg. Med. Chem. Lett., 2003, 13, 1897-1901. Giannini, G.; Marzi, M.; Marzo, M.D.; Battistuzzi, G.; Pezzi, R.; Brunetti, T.; Cabri, W.; Vesci, L.; Pisano, C. Exploring bis(indolyl)methane moiety as an alternative and innovative CAP group in the design of histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett., 2009, 19, 2840-2843. Tang, W.; Luo, G.; EF, Bradner, J.E.; Schreiber, S.L. Discovery of histone deacetylase 8 selective inhibitors. Bioorg. Med. Chem. Lett., 2011, 21, 2601-2605. Salisbury, C.M.; Cravatt, B.F. Optimization of activity-based probes for proteomic profiling of histone deacetylase complexes. J. Am. Chem. Soc., 2008, 130, 2184-2194. Kozikowski, A.P.; Tapadar, S.; Luchini, D.N.; Kim, K.H.; Billadeau, D.D. Use of the nitrile oxide cycloaddition (NOC) reaction for molecular probe generation.; a new class of enzyme selective histone deacetylase inhibitors (HDACIs) showing picomolar activity at HDAC6. J. Med. Chem., 2008, 51, 4370-4373. He, B.; Velaparthi, S.; Pieffet, G.; Pennington, C.; Mahesh, A.; Holzle, DL.; Brunsteiner, M.; Breemen, R.; Blond, S.Y.; Petukhov, P.A. Binding ensemble profiling with photoaffinity labeling (beprofl) approach.; mapping the binding poses of hdac8 inhibitors. J. Med. Chem., 2009, 52, 7003-7013. Neelarapu, R.; Holzle, D.L.; Velaparthi, S.; Bai, H.; Brunsteiner, M.; Blond, S.Y.; Petukhov, P.A. Design.; synthesis.; docking.; and biological evaluation of novel diazide-containing isoxazole- and pyrazole-based histone deacetylase probes. J. Med. Chem., 2011, 54, 4350-4364. Ommeslaeghe, K.V.; Elaut, G.; Brecx, V.; Papeleu, P.; Iterbeke, K.; Geerlings, P.; Tourwe, D.; Rogiers, V. Amide Analogs of TSA.; Synthesis.; Binding Mode Analysis and HDAC Inhibition. Bioorg. Med. Chem. Lett., 2003, 13, 1861-1864. Bouchain, G.; Delorme, D. Novel hydroxamate and anilide derivatives as potent histone deacetylase inhibitors.; synthesis and antiproliferative evaluation. Curr. Med. Chem., 2003, 10, 2359-2372. Jung, M.; Brosch, G.; Kolle, D.; Scherf, H.; Gerhauser, C.; Loidl, P.J. Amide analogues of trichostatin A as inhibitors of histone deacetylase and inducers of terminal cell differentiation. J. Med. Chem., 1999, 42, 4669-4679. Jung, M.; Hoffmann, K. Brosch, G. Loidl, P. Aalogues of trichostatin aand trapoxin B as histone deacetylase inhibitor. Bioorg. Med. Chem. Lett., 1997, 7, 1655-1658. Remiszewski, S.W. The Discovery of NVP-LAQ824.; From Concept to Clinic. Curr. Med. Chem., 2003, 10, 2393-2402. Remiszewski, S.W.; Sambucetti, L.C.; Atadja, P.; Bair, K.W.; Cornell, W.D.; Green, M.A.; Howell, K.L.; Jung, M.; Kwon, P.; Trogani, N.; Walker, H. Inhibitors of human histone deacetylase.; synthesis and enzyme and cellular activity of straight chain hydroxamates. J. Med. Chem., 2002, 45, 753-757. Woo, S.H.; Frechette, S.; Khalil, E.A.; Bouchain, G.; Vaisburg, A.; Bernstein, N.; Moradei, O.; Leit, S.; Allan, M.; Fournel, M.; Trachy-Bourget, M.C.; Li, Z.; Besterman, J.M.; Delorme, D. Structurally simple trichostatin A-like straight chain hydroxamates as potent histone deacetylase inhibitors. J. Med. Chem., 2002, 45, 2877-2885. Zhang, Y.; Feng, J.; Jia, Y.; Xu, Y.; Liu, C.; Fang, H.; Xu, W. Design, synthesis and primary activity assay of tripeptidomimetics as histone deacetylase inhibitors with linear linker and branched cap group. Eur. J. Med. Chem., 2011, 46, 5387-5397. Curtin, M.L.; Garland, R.B.; Heyman, H.R.; Frey, R.R.; Michaelides, M.R.; Li, J.; Pease, LJ.; Glaser, KB.; Marcotte, PA.; Davidsen, SK. Succinimide Hydroxamic Acids as Potent Inhibitors of Histone Deacetylase (HDAC). Bioorg. Med. Chem. Lett., 2002, 12, 2919-2923. Wittich, S.; Scherf, H.; Xie, C.; Brosch, G.; Loidl, P.; Gerha, C.; Jung, M. Structure activity relationships on phenylalaninecontaining inhibitors of histone deacetylase.; in vitro enzyme inhibition.; induction of differentiation.; and inhibition of proliferation in friend leukemic cells. J. Med. Chem., 2002, 45, 3296-3309. Sundarapandian, T.; Shalini, J.; Sugunadevi, S.; Woo, L.K. Docking-enabled pharmacophore model for histone deacetylase 8 inhibitors and its application in anti-cancer drug discovery. J. Mol. Graphics Modell., 2010, 29, 382-395. Huang, W.J.; Chen, C.C.; Chao, S.W.; Yu, C.C.; Yui, Y.C.; Guh, J.H.; Lin, Y.C.; Kuo, C.I.; Yang, P.; Chang, C.I. Synthesis and

Hydroxamic Acid Based HDAC Inhibitors

[51]

[52]

[53]

[54]

[55]

[56]

[57]

[58]

[59]

[60]

[61] [62]

[63] [64] [65]

[66]

evaluation of aliphatic-chain hydroxamates capped with osthole derivatives as histone deacetylase inhibitors. Eur. J. Med. Chem., 2011, 46, 4042-4049. Cai, X.; Zhai, H.X.; Wang, J.; Forrester, J.; Qu, H.; Yin, L.; Lai, C.J.; Bao, R.; Qian, C. Discovery of 7-(4-(3-ethynylphenylamino)7-methoxyquinazolin-6-yloxy)-N-hydroxy-heptanamide (CUDc101) as a potent multi-acting HDAC.; EGFR.; and HER2 inhibitor for the treatment of cancer. J. Med. Chem., 2010, 53, 2000-2009. Belvedere, S.; Witter, DJ.; Yan, J.; Secrist, J.P.; Richona, V.; Millera, T.A. Aminosuberoyl hydroxamic acids (ASHAs).; A potent new class of HDAC inhibitors. Bioorg. Med. Chem. Lett., 2007, 17, 3969-3971. Wang, H.; Lim, Z.Y.; Zhou, Y.; Ng, M.; Lu, T.; Lee, K.; Sangthongpitag, K.; Goh, K.C.; Wang, X.; Wub, X.; Khng, H.H.; Goh, S.K.; Ong, W.C.; Bonday, Z.; Sun, E.T. Acylurea connected straight chain hydroxamates as novel histone deacetylase inhibitors, Synthesis, SAR, and in vivo antitumor activity. Bioorg. Med. Chem. Lett., 2010, 20, 3314-3321. Marson, C.M.; Mahadevan, T.; Dines, J.; Sengmany, S.; Morrell, J.M.; Alao, J.P.; Joel, S.P.; Vigushin, D.M.; Coombes, R.C. Structure–activity relationships of aryloxyalkanoic acid hydroxyamides as potent inhibitors of histone deacetylase. Bioorg. Med. Chem. Lett., 2007, 17, 136-141. Glaser, KB.; Li, J.; Aakre, M.E.; Morgan, D.W.; Sheppard, G.; Stewart, K.D.; Pollock, J.; Lee, P.; O'Connor, C.Z.; Anderson, S.N.; Mussatto, D.J.; Wegner, C.W.; Moses, H.L. Transforming growth factor beta mimetics.; discovery of 7-4-(4cyanophenyl)phenoxy.-heptanohydroxamic acid.; a biaryl hydroxamate inhibitor of histone deacetylase. Mol. Cancer Ther., 2002, 1, 759–768. Marek, L.; Hamacher, A.; Hansen, F.K.; Kuna, K.; Gohlke, H.; Kassack, M.U.; Kurz, T. Histone deacetylase (HDAC) inhibitors with a novel connecting unit linker region reveal a selectivity profile for HDAC4 and HDAC5 with improved activity against chemoresistant cancer cells. J. Med. Chem., 2013, 56, 427-436. Chen, P.C.; Patil, V.; Guerrant, W.; Green, P.; Oyelere, A.K. Synthesis and structure–activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group. Bioorg. Med. Chem., 2008, 16, 4839-4853. Dai, Y.; Guo, Y.; Curtin, M.L.; Li, J.; Pease, L.J.; Guo, J.; Marcotte, P.A.; Glaser, K.B.; Davidsen, S.K.; Michaelides, M.R. A Novel Series of Histone Deacetylase Inhibitors Incorporating Hetero Aromatic Ring Systems as Connection Units. Bioorg. Med. Chem. Lett., 2003, 13, 3817-3820. Bigioni, M.; Ettorre, A.; Felicetti, P.; Mauro, S.; Rossi, C.; Maggi, C.A.; Marastoni, E.; Binaschi, M.; Parlani, M.; Fattori, D. Set-up of a new series of HDAC inhibitors: the 5,11-dihydrodibenzo[b,e] azepin-6-ones as privileged structures. Bioorg. Med. Chem. Lett., 2012, 22, 5360-5362. Grolla, A.A.; Podesta, V.; Chini, M.G.; Micco, SD.; Vallario, A.; Genazzani, A.A Canonico, P.L.; Bifulco, G.; Tron, G.C.; Sorba, G.; Pirali, T. Synthesis.; biological evaluation.; and molecular docking of ugi products containing a zinc-chelating moiety as novel inhibitors of histone deacetylases. J. Med. Chem., 2009, 52, 2776-2785. Flipo, M.; Charton, J.; Hocine, A.; Dassonneville, S.; Deprez, B.; Poulain, R.D. Hydroxamates, relationships between structure and plasma stability. J. Med. Chem., 2009, 52, 6790-6802. Choi, S.E.; Weerasinghe, S.V.W.; Pflum, M.K.H. The structural requirements of histone deacetylase inhibitors.; Suberoylanilide hydroxamic acid analogs modified at the C3 position display isoform selectivity. Bioorg. Med. Chem. Lett., 2011, 21, 6139-6142. Chowdhury, N.; Dasgupta, S.; Singh, N.D.P. Photoinduced DNA cleavage by anthracene based hydroxamic acids. Bioorg. Med. Chem. Lett., 2012, 22, 4668-4671. Luo, Y.; Liu, H.M.; Su, M.B.; Sheng, L.; Zhou, Y.B.; Li, J.; Lu, W. Synthesis and biological evaluation of piperamide analogs as HDAC inhibitors. Bioorg. Med. Chem. Lett., 2011, 21, 4844-4846. Marson, C.M.; Savy, P.; Rioja, A.S.; Mahadevan, T.; Mikol, C.; Veerupillai, A.; Nsubuga, E.; Chahwan, A.; Joel, S.P. Aromatic Sulfide Inhibitors of Histone Deacetylase Based on Arylsulfinyl2.;4-hexadienoic Acid Hydroxyamides. J. Med. Chem., 2006, 49, 800-805. Pabba, C.; Gregg, B.T.; Douglas, B.K.; Chen, Z.J.; Judkins, A. Design and synthesis of aryl ether and sulfone hydroxamic acids as potent histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett., 2011, 21, 324-328.

Current Medicinal Chemistry, 2014, Vol. 21, No. 1 [67]

[68] [69]

[70]

[71]

[72]

[73]

[74]

[75]

[76]

[77]

[78] [79]

[80]

[81]

21

Charrier, C.; Clarhaut, J.; Gesson, J.P.; Estiu, G.; Wiest, O.; Roche, J.; Bertrand, P. Synthesis and modeling of new benzofuranone histone deacetylase inhibitors that stimulate tumor suppressor gene expression. J. Med. Chem., 2009, 52, 3112-3115. Arts, J.; Schepper, S.; Emelen, K.V. Histone deacetylase inhibitors from chromatin remodeling to experimental cancer therapeutics. Curr. Med. Chem., 2003, 10, 2343-2350. Lavoie, R.; Bouchain, G.; Frechette, S.; Woo, S.H.; Khalil, E.A.; Leit, S.; Fournel, M.; Yan, P.T.; Trachy-Bourget, M.C.; Beaulieu, C.; Li, Z.; Besterman, J.; Delorme, D. Design and synthesis of a novel class of histone deacetylase inhibitors. Bioorg. Med. Chem. Lett., 2001, 11, 2847-2850. Charles, M.M.; Serradji, N.; Rioja, A.S.; Gastaud, S.P.; Alao, J.P.; Coombesb, R.C.; Vigushinb, D.M. Stereodefined and polyunsaturated inhibitors of histone deacetylase based on (2E.;4E)-5arylpenta-2.;4-dienoic acid hydroxyamides. Bioorg. Med. Chem. Lett., 2004, 14, 2477-2481. Vaisbure, A.; Bernstein, N.; Frechette, S.; Allan, M.; Khalil, E.A.; Leit, S.; Moradei, O.; Bouchain, G.; Wang, J.; Woo, S.H.; Fournel, M.; Yan, P.T.; Bourget, M.C.T.; Kalita, A.; Li, Z.; Macleod, A.R.; Bestermanab, J.M.; Delormea, D. (2-Amino-phenyl)-amides of !substituted alkanoic acids as new histone deacetylase inhibitors. Bioorg. Med. Chem. Lett., 2004, 14, 283-287. Bouchain, G.; Leit, S.; Frechette, S.; Khalil, E.A.; Lavoie, R.; Moradei, O.; Woo, SH.; Fournel, M.; Yan, P.T.; Kalita, A.; Bourget, M.C.T.; Beaulieu, C.; Li, Z.; Robert, M.F.; MacLeod, A.R.; Besterman, J.M.; Delorme, D. Development of potential antitumor agents synthesis and biological evaluation of a new set of sulfonamide derivatives as histone deacetylase inhibitors. J. Med. Chem., 2003, 46, 820-830. Dallavalle, S.; Cincinelli, R.; Nannei, R.; Merlini, L.; Morini, G.; Penco, S.; Pisano, C.; Vesci, L.; Barbarino, M.; Zuco, V.; Cesare, M.D.; Zunino, F. Design.; synthesis and evaluation of biphenyl-4yl-acrylohydroxamic acid derivatives as histone deacetylase (HDAC) inhibitors. Eur. J. Med. Chem., 2009, 44, 1900-1912. Kim, D.K.; Lee, J.Y.; Kim, J.S.; Ryu, J.H.; Choi, J.Y.; Lee, J.W.; Im, G.J.; Kim, T.K.; Seo, J.W.; Park, H.J.; Yoo, J.; Park, J.H.; Kim, T.Y.; Bang, Y.J. Synthesis and biological evaluation of 3-(4substituted-phenyl)-n-hydroxy-2-propenamides.; a new class of histone deacetylase inhibitors. J. Med. Chem., 2003, 46, 5745-5751. Smil, D.V.; Manku, S.; Chantign,YA.; Leit, S.; Wahhab, A.; Yan, T.P.; Fournel, M.; Maroun, C.; Li, Z.; Lemieux, A.M.; Nicolescu, A.; Rahil, J.; Lefebvre, S.; Panetta, A.; Besterman, J.M.; Déziel, R. Novel HDAC6 isoform selective chiral small molecule histone deacetylase inhibitors. Bioorg. Med. Chem. Lett., 2009, 19, 688692. Shultz, MD.; Cao, X.; Chen, C.H.; Cho, Y.S.; Davis, N.R.; Eckman, J.; Fan, J.; Fekete, A.; Firestone, B.; Flynn, J.; Green, J.; Growney, JD.; Holmqvist, M.; Hsu, M.; Jansson, D.; Jiang, L.; Kwon, P.; Liu, G.; Lombardo, F.; Lu, Q.; Majumdar, D.; Meta, C.; Perez, L.; Pu, M.; Ramsey, T.; Remiszewski, S.; Skolnik, S.; Traebert, M.; Urban, L.; Uttamsingh, V.; Wang, P.; Whitebread, S.; Whitehead, L.; Neale, Y.Y.; Yao, Y.M.; Zhou, L.; Atadja, P. Optimization of the in vitro cardiac safety of hydroxamate-based histone deacetylase inhibitors. J. Med. Chem., 2011. 54, 4752-4772. Chen, L.; Petrelli, R.; Gao, G.; Wilson, D.J.; McLean, G.T.; Jayaram, H.N.; Sham, Y.Y.; Pankiewicz, K.W. Dual inhibitors of inosine monophosphate dehydrogenase and histone deacetylase based on a cinnamic hydroxamic acid core structure. Bioorg. Med. Chem., 2010, 18, 5950-5964. Curtin, M.; Glaser, K. Histone Deacetylase Inhibitors.; The Abbott Experience. Curr. Med. Chem., 2003, 10, 2373-2392. Lu, Q.; Yang, Y.T.; Chen, C.S.; Davis, M.; Byrd, J.C.; Etherton, M.R.; Umar, A.; Chen, C.S. Zn2+-chelating motif-tethered shortchain fatty acids as a novel class of histone deacetylase inhibitors. J. Med. Chem., 2004, 47, 467-474. Mai, A.; Massa, S.; Rotili, D.; Simeoni, S.; Ragno, R.; Botta, G.; Nebbioso, A.; Miceli, M.; Altucci, L.; Brosch, G. Synthesis and biological properties of novel.; uracil-containing histone deacetylase inhibitors. J. Med. Chem., 2006, 49, 6046-6056. Mahboobi, S.; Sellmer, A.; Hocher, H.; Garhammer, C.; Pongratz, H.; Maier, T.; Ciossek, T.; Beckers, T. 2-Aroylindoles and 2aroylbenzofurans with N-hydroxyacrylamide substructures as a novel series of rationally designed histone deacetylase inhibitors. J. Med. Chem., 2007, 50, 4405-4418.

22 Current Medicinal Chemistry, 2014, Vol. 21, No. 1 [82]

[83]

[84]

[85]

[86]

[87]

[88]

[89]

[90]

[91]

[92] [93]

[94]

[95]

[96]

[97]

Cheng, X.C.; Wang, R.L.; Dong, Z.K.; Li, J.; Li, Y.Y.; Li, R.R. Design, synthesis and evaluation of novel metalloproteinase inhibitors based on l-tyrosine scaffold. Bioorg. Med. Chem., 2012, 20, 5738-5744. Yoon, H.C.; Choi, E.; Park, JE.; Cho, M.; Seo, J.J.; Ohb, S.J.; Kang, S.J. Property based optimization of -lactam HDAC inhibitors for metabolic stability. Bioorg. Med. Chem. Lett., 2010, 20, 6808-6811. Kim, H.M.; Ryu, D.K.; Choi, Y.; Park, B.W.; Lee, K.; Han, S.B.; Lee, CW.; Kang, M.R.; Kang, J.S.; Boovanahalli, S.K.; Park, S.K.; Han, J.W.; Chun, T.G.; Lee, H.Y.; Nam, K.Y.; Choi, E.H.; Han, G. Structure-activity relationship studies of a series of novel -lactambased histone deacetylase inhibitors. J. Med. Chem., 2007, 50, 2737-2741. Kim, H.M.; Hong, S.H.; Kim, M.S.; Lee, C.W.; Kang, J.S.; Lee, K.; Park, S.K.; Han, J.W.; Lee, H.Y.; Choi, Y.; Kwon, H.J.; Hanb, G. Modification of cap group in -lactam-based histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett., 2007, 17, 62346238. Choi, E.; Lee, C.; Park, J.E.; Seo, J.J.; Cho, M.; Kang, J.S.; Kim, H.M. Structure and property based design.; synthesis and biological evaluation of -lactam based HDAC inhibitors. Bioorg. Med. Chem. Lett., 2011, 21, 1218-1221. Rossi, C.; Porcelloni, M., D’Andrea, P.; Fincham, CI.; Ettorre, A.; Mauro, S.; Squarcia, A.; Bigioni, M.; Parlani, M.; Nardelli, F.; Binaschi, M.; Maggi, C.A.; Fattori, D. Alkyl piperidine and piperazine hydroxamic acids as HDAC inhibitors. Bioorg. Med. Chem. Lett., 2011, 21, 2305-2308. Chetan, B.; Bunha, M.; Jagrat, M.; Sinha, B.N.; Saiko, P.; Graser, G.; Szekeres, T.; Raman, G.; Rajendran, P.; Moorthy, D.; Basu, A.V. Design.; synthesis and anticancer activity of piperazine hydroxamates and their histone deacetylase (HDAC) inhibitory activity. Bioorg. Med. Chem. Lett., 2010, 20, 3906-3910. Rajak, H.; Agarawal, A.; Parmar, P.; Thakur, BS.; Veerasamy, R.; Sharma, C.P.; Kharya, M.D. 2.;5-Disubstituted-1.;3.;4oxadiazoles/thiadiazole as surface recognition moiety.; Design and synthesis of novel hydroxamic acid based histone deacetylase inhibitors. Bioorg. Med. Chem. Lett., 2011, 21, 5735-5738. Uesato, S.; Kitagawa, M.; Nagaoka, Y.; Maeda, T.; Kuwajima, H.; Yamori, T. Novel histone deacetylase inhibitors.; N-hydroxycarboxamides possessing a terminal bicyclic aryl group. Bioorg. Med. Chem. Lett., 2002, 12, 1347-1349. Lee, C.;Choi, E.; Cho, M.; Lee, B.; Oh, S.J.; Park, S.K.; Lee, K.; Kim, H.M.; Han, G. Structure and property based design, synthesis and biological evaluation of -lactam based HDAC inhibitors: Part II. Bioorg. Med. Chem. Lett., 2012, 22, 4189-4192. Conti, P.; Tamborini, L.; Pinto, A.; Sola, L.; Ettari, R.; Mercurio, C.; Micheli, C.D. Design and synthesis of novel isoxazole-based HDAC inhibitors. Eur. J. Med. Chem., 2010, 45, 4331-4338. Tapadar, S.; He, R.; Luchini, D.N.; Billadeau, D.D.; Kozikowski, A.P. Isoxazole moiety in the linker region of HDAC inhibitors adjacent to the Zn-chelating group.; Effects on HDAC biology and antiproliferative activity. Bioorg. Med. Chem. Lett., 2009, 19, 3023-3026. Hong Su.; Nebbioso A.; Carafa V.; Chen Y.; Yang B.; Altucci L.; You Q. Design, synthesis and biological evaluation of novel compounds with conjugated structure as anti-tumor agents. Bioorg. Med. Chem., 2008, 16, 7992-8002. Price, S.; Bordogna, W.; Bull, R.J.; Clark, D.E.; Crackett, P.H.; Dyke, H.J.; Gill, M.; Harris, N.V.; Gorski, J.; Lloyd, J.; Lockey, P.M.; Mullett, J.; Roach, A.G.; Roussel, F.; White, A.B. Identification and optimisation of a series of substituted 5-(1H-pyrazol-3-yl)thiophene-2-hydroxamic acids as potent histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett., 2007, 17, 370-375. Price, S.; Bordogn, W.; Braganza, R.; Bull, R.J.; Dyke, H.J.; Gardan, S.; Gill, M.; Harris, N.V.; Heald, R.A.; Heuvel, Mvd.; Lockey, P.M.; Lloyd, J.; Molina, A.G.; Roach, A.G.; Roussel, F.; Sutton, J.M.; White, A.B. Identification and optimisation of a series of substituted 5-pyridin-2-yl-thiophene-2-hydroxamic acids as potent histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett., 2007, 17, 363-369. Mai, A.; Massa, S.; Ragno, R.; Esposito, M.; Sbardella, G.; Nocca, G.; Scatena, R.; Jesacher, F.; Loidl, P.; Brosch, G. Binding mode analysis of 3-(4-benzoyl-1-methyl-1h-2-pyrrolyl)-n-hydroxy-2propenamide.; a new synthetic histone deacetylase inhibitor induc-

Rajak et al.

[98]

[99]

[100]

[101]

[102]

[103]

[104]

[105]

[106]

[107]

[108]

[109]

[110]

[111] [112]

ing histone hyperacetylation.; growth inhibition.; and terminal cell differentiation. J. Med. Chem., 2002, 45, 1778-1784. Mai, A.; Massa, S.; Cerbara, I.; Valente, S.; Ragno, R.; Bottoni, P.; Scatena, R.; Loidl, P.; Brosch, G. 3-(4-Aroyl-1-methyl-1H-2pyrrolyl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors 2 effect of pyrrole-C2 and/or -C4 substitutions on biological activity. J. Med. Chem., 2004, 47, 10981109. Mai, A.; Massa, S.; Pezzi, R.; Simeoni, S.; Rotili, D.; Nebbioso, A.; Scognamiglio, A.; Altucci, L.; Loidl, P.; Brosch, G. Class II (IIa)selective histone deacetylase inhibitors 1 synthesis and biological evaluation of novel (aryloxopropenyl)pyrrolyl hydroxyamides. J. Med. Chem., 2005, 48, 3344-3353. Ragno, R.; Mai, A.; Massa, S.; Cerbara, I.; Valente, S.; Bottoni, P.; Scatena, R.; Jesacher, F.; Loidl, P.; Brosch, G. 3-(4-Aroyl-1methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors 3 discovery of novel lead compounds through structure-based drug design and docking studies. J. Med. Chem., 2004, 47, 1351-1359. Massa, S.; Artico, M.; Corelli, F.; Mai, A.; Santo, RD.; Cortes, S.; Marongiu, ME.; Pani, A.; La Colla, P. Synthesis and antimicrobial and cytotoxic activities of pyrrole-containing analogs of trichostatin A. J. Med. Chem., 1990, 33, 2845-2849. Mai, A.; Massa, S.; Pezzi, R.; Rotili, D.; Loidl, P.; Brosch, G. Discovery of (aryloxopropenyl)pyrrolyl hydroxyamides as selective inhibitors of class IIa histone deacetylase homologue HD1-A. J. Med. Chem., 2003, 46, 4826-4829. Hou, J.; Feng, C.; Li, Z.; Fang, Q.; Wang, H.; Gu, G.; Shi, Y.; Liu, P.; Xu, F.; Yin, Z.; Shen, J.; Wang, P. Structure-based optimization of click-based histone deacetylase inhibitors. Eur. J. Med. Chem., 2011, 46, 3190-3200. Lai, M.J.; Huang, H.L.; Pan, S.L.; Liu, Y.M.; Peng, C.Y.; Lee, H.Y.; Yeh, T.K.; Huang, P.H.; Teng,C.M.; Chen, C.S.; Chuang, H.Y.; Liou, J.P. Synthesis and biological evaluation of 1arylsulfonyl-5-(N-hydroxyacrylamide) indoles as potent histone deacetylase inhibitors with antitumor activity in vivo. J. Med. Chem., 2012, 55, 3777-3791. Lee, S.; Shinji, C.; Ogura, K.; Shimizu, M.; Maeda, S.; Sato, M.; Yoshida, M.; Hashimotoa, Y.; Miyachia, H. Design.; synthesis.; and evaluation of isoindolinone-hydroxamic acid derivatives as histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett., 2007, 17, 4895-4900. Wang, H.; Yu, N.; Song, H.; Chen, D.; Zou, Y.; Deng, W.; Lye, PL.; Chang, J.; Ng, M.; Blanchard, S.; Sun, ET.; Sangthongpitag, K.; Wang, X.; Goh, K.C.; Wu, X.; Khng, H.H.; Fang, L.; Goh, S.K.; Ong, W.C.; Bonday, Z.; Stünkel, W.; Poulsen, A.; Entzeroth, M. N-Hydroxy-1.;2-disubstituted-1H-benzimidazol-5-yl acrylamides as novel histone deacetylase inhibitors.; Design.; synthesis.; SAR studies.; and in vivo antitumor activity. Bioorg. Med. Chem. Lett., 2009, 19, 1403-1408. Shinji, C.; Nakamura, T.; Maeda, S.; Yoshida, M.; Hashimotoa, Y.; Miyachia, H. Design and synthesis of phthalimide-type histone deacetylase inhibitors. Bioorg. Med. Chem. Lett., 2005, 15, 44274431. Zhang, Y.; Feng, J.; Liu, C.; Fang, H.; Xu, W. Design.; synthesis and biological evaluation of tyrosine-based hydroxamic acid analogs as novel histone deacetylases (HDACs) inhibitors. Bioorg. Med. Chem., 2011, 19, 4437-4444. Donald, A.D.G.; Clark, V.L.; Patel, S.; Day, F.A.; Martin, G.; Rowlands, Wibata, J.; Stimson, L.; Hardcastle, A.; Eccles, S.A.; McNamara, D.; Needham, L.A.; Raynaud, F.I.; Aherne, W.; Moffat, D.F. Design and synthesis of novel pyrimidine hydroxamic acid inhibitors of histone deacetylases. Bioorg. Med. Chem. Lett., 2010, 20, 6657-6660. Suzuki,T.; Ota, Y.; Ri, M.; Bando, M.; Gotoh, A.; Itoh, Y.; Tsumoto, H.; Tatum, P.R.; Mizukami, T.; Nakagawa,H.; Iida, S.; Ueda, R.; Shirahige, K.; Miyata, N. rapid discovery of highly potent and selective inhibitors of histone deacetylase 8 using click chemistry to generate candidate libraries. J. Med. Chem., 2012, 55, 95629575. Wang, H.; Dymock, B.W. New patented histone deacetylase inhibitors. Expert Opin. Ther. Patents, 2009, 19, 1727-1757. Varasi, M.; Thaler, F.; Abate, A.; Bigogno, C.; Boggio, R.; Carenzi, G.; Cataudella, T.; Zuffo, R.D.; Fulco, M.C.; Rozio, M.G.; Mai, A.; Dondio, G.; Minucci, S.; Mercurio, C. Discovery, synthesis, and pharmacological evaluation of spiropiperidine hydroxamic

Hydroxamic Acid Based HDAC Inhibitors

[113]

[114]

[115] [116] [117]

[118]

Current Medicinal Chemistry, 2014, Vol. 21, No. 1

acid based derivatives as structurally novel histone deacetylase (HDAC) inhibitors. J. Med. Chem., 2011, 54, 3051-3064. Glenn, M.P.; Kahnberg, P.; Boyle, G.M.; Hansford, K.A.; Hans, D.; Martyn, A.C.; Parsons, P.G.; Fairlie, D.P. Antiproliferative and phenotype-transforming antitumor agents derived from cysteine. J. Med. Chem., 2004, 47, 2984-2994. Kahnberg, P.; Lucke, A.J.; Glenn, M.P.; Boyle, G.M.; Tyndall, J.D.A.; Parsons, P.G.; Fairlie, D.P. design.; synthesis.; potency.; and cytoselectivity of anticancer agents derived by parallel synthesis from -aminosuberic acid. J. Med. Chem., 2006, 49, 7611-7622. Shen, J.; Woodward, R.; Kedenburg, J.P.; Liu, X.; Chen, M.; Fang, L.; Sun, D.; Wang, P.G. Histone Deacetylase Inhibitors through Click Chemistry. J. Med. Chem., 2008, 51, 7417-7427. Zhang, Y.; Fang, H.; Jiao, J.; Xu, W. The Structure and Function of Histone Deacetylases.; The Target for Anti-cancer Therapy. Curr. Med. Chem., 2008, 15, 2840-2849. Wang, H.; Yu, N.; Chen, D.; Lee, K.C.L.; Lye, P.L.; Chang, J.W.W.; Deng, W.; Ng, M.C.Y.; Lu, T.; Khoo, M.L.; Poulsen, A.; Sangthongpitag, K.; Wu, X.; Hu, C.; Goh, K.C.; Wang, X.; Fang, L.; Goh, K.L.; Khng, H.H.; Goh, S.K.; Yeo, P.; Liu, X.; Bonday, Z.; Wood, J.M.; Dymock, B.W.; Ethirajulu, K.; Sun, E.T. Discovery of (2E)-3-{2-Butyl-1-2-(diethylamino)ethyl.-1Hbenzimidazol5-yl}-N-hydroxyacrylamide (SB939.;an Orally Active Histone Deacetylase Inhibitor with a Superior Preclinical Profile. J. Med. Chem., 2011, 54, 4694-4720. Varghese, S.; Gupta, D.; Baran, T.; Jiemjit, A.; Gore, S.D.; Casero, R.A.; Woster, P.M. Alkyl-substituted polyaminohydroxamic acids.;

Received: July 08, 2012

Revised: June 02, 2013

Accepted: July 23, 2013

[119]

[120] [121]

[122]

[123]

[124]

23

a novel class of targeted histone deacetylase inhibitors. J. Med. Chem., 2005, 48, 6350-6365. Gediya, L.K.; Chopra, P.; Purushottamachar, P.; Maheshwari, N.; Njar, C.O. A new simple and high-yield synthesis of suberoylanilide hydroxamic acid and its inhibitory effect alone or in combination with retinoids on proliferation of human prostate cancer cells. J. Med. Chem., 2005, 48, 5047-5051. Inks, E.S.; Josey, B.J.; Jesinkey, S.R.; Chou, C.J. A novel class of small molecule inhibitors of HDAC6. ACS Chem. Biol., 2012, 17, 331-339. Guan, P.; Sun, F.; Hou, X.; Wang, F.; Yi, F.; Xu, W.; Fang, H. Design, synthesis and preliminary bioactivity studies of 1,3,4thiadiazole hydroxamic acid derivatives as novel histone deacetylase inhibitors. Bioorg. Med. Chem., 2012, 20, 3865-3872. Blanquart, C.; Francois, M.; Charrier, C.; Bertrand, P.; Gregoire, M. Pharmacological characterization of histone deacetylase inhibitor and tumor cell-growth inhibition properties of new benzofuranone compounds. Curr. Cancer Drug Targets, 2011, 11, 919-928. Rodriqueza, M.; Aquinoa, M.; Brunoa, I.; Martinoa, G.D.; Taddeib, M.; Gomez-Paloma, L. Chemistry and biology of chromatin remodeling agents.; state of art and future perspectives of HDAC inhibitors. Curr. Med. Chem., 2006, 13, 1119-1139. Suzuki, T.; Nagano, Y.; Kouketsu, A.; Matsuura, A.; Maruyama, S.; Kurotaki, M.; Nakagawa, H.; Miyata, N. Novel inhibitors of human histone deacetylases.; design.; synthesis.; enzyme inhibition.; and cancer cell growth inhibition of SAHA-based nonhydroxamates. J. Med. Chem., 2005, 48, 1019-1032.