Thiazolidinedione “Magic Bullets” Simultaneously Targeting PPARγ and HDACs: Design, Synthesis, and Investigations of their In Vitro and In Vivo Antitumor Effects

Kalpana Tilekar; Jessica D Hess; Neha Upadhyay; Alessandra Lo Bianco; Markus Schweipert; Antonio Laghezza; Fulvio Loiodice; Franz-Josef Meyer-Almes; Renato J Aguilera; Antonio Lavecchia; C S Ramaa

doi:10.1021/acs.jmedchem.1c00491

. Author manuscript; available in PMC: 2024 Mar 11.

Published in final edited form as: J Med Chem. 2021 May 18;64(10):6949–6971. doi: 10.1021/acs.jmedchem.1c00491

Thiazolidinedione “Magic Bullets” Simultaneously Targeting PPARγ and HDACs: Design, Synthesis, and Investigations of their In Vitro and In Vivo Antitumor Effects

Kalpana Tilekar ¹, Jessica D Hess ², Neha Upadhyay ³, Alessandra Lo Bianco ⁴, Markus Schweipert ⁵, Antonio Laghezza ⁶, Fulvio Loiodice ⁷, Franz-Josef Meyer-Almes ⁸, Renato J Aguilera ⁹, Antonio Lavecchia ¹⁰, C S Ramaa ¹¹

PMCID: PMC10926851 NIHMSID: NIHMS1959306 PMID: 34006099

Abstract

Monotargeting anticancer agents suffer from resistance and target nonspecificity concerns, which can be tackled with a multitargeting approach. The combined treatment with HDAC inhibitors and PPARγ agonists has displayed potential antitumor effects. Based on these observations, this work involves design and synthesis of molecules that can simultaneously target PPARγ and HDAC. Several out of 25 compounds inhibited HDAC4, and six compounds acted as dual-targeting agents. Compound 7i was the most potent, with activity toward PPARγ EC₅₀ = 0.245 μM and HDAC4 IC₅₀ = 1.1 μM. Additionally, compounds 7c and 7i were cytotoxic to CCRF-CEM cells (CC₅₀ = 2.8 and 9.6 μM, respectively), induced apoptosis, and caused DNA fragmentation. Furthermore, compound 7c modulated the expression of c-Myc, cleaved caspase-3, and caused in vivo tumor regression in CCRF-CEM tumor xenografts. Thus, this study provides a basis for the rational design of dual/multitargeting agents that could be developed further as anticancer therapeutics.

Graphical Abstract

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INTRODUCTION

Cancer is the most prevalent disease worldwide and is regulated by genetic and epigenetic mechanisms. The major challenge in anticancer drug discovery is to bring about a therapeutic approach capable of attenuating malignant cells without damaging normal cells. Thus, there exist two fundamentals of a drug, viz., target specificity and potency. The clinical effectiveness of recent monotargeted drugs are transitory because of unexpected resistance and target nonspecificity due to tumor heterogeneity.^1,2 To overcome these concerns, an alternative strategy of multitargeting can be applied to hit multiple cancer hallmarks and achieve the desired pharmacological efficiency with reduced detrimental effects such as drug–drug interactions, unforeseen side-effects, and poor patient compliance.^3–6 Moreover, in a multitarget approach, the concept of “magic bullets” exist—which are single agents with target specificity and high potency.⁷

In the development and progression of several malignancies, epigenetics contributes significantly. Tumor cell activation is effectively regulated by epigenetic mechanisms which facilitate escape from chemotherapy; thus, the recent focus of anticancer drug discovery has been directed to epigenetic targets.^8,9 There are numerous enzymes involved in epigenetic regulation; for example, histone deacetylases (HDACs) are indispensable in regulation of gene transcription and cellular homeostasis events.^10–13 Also, aberrant expression of HDACs has been linked to a variety of solid and hematological malignancies, neurological disorders, and inflammation.¹⁴ There are various FDA-approved HDAC inhibitors such as SAHA, belinostat, panobinostat, and romidepsin, as well as various agents under clinical studies.¹⁵ However, the use of these inhibitors as a monotherapy against solid tumors has shown limited efficacy; thus, the development of HDAC inhibitors with multitarget specificity has been studied extensively.^16–22

PPARs (peroxisome proliferator-activated receptors) are ligand-activated transcription factors that play a key role in the regulation of a large number of genes whose products are directly or indirectly involved in glucose homeostasis and lipid metabolism. The subtype PPARγ is the most widely studied and acts as a key factor in various metabolic processes playing an important role in the regulation of insulin tissue sensitivity and in the management of glucose and lipid uptake and storage.²³ PPARγ is the receptor of well-known antidiabetic insulin sensitizer drugs rosiglitazone and pioglitazone, which belong to the thiazolidinedione (TZD) class.²⁴ Apart from its role in the cardiovascular system, PPARγ is vital to cancer cell growth regulation. A large body of evidence shows that agonistic PPARγ ligands exert antitumorigenic effects against a variety of neoplastic cell types, both in vivo and in vitro.^25–28 For instance, efatutazone is indicated in thyroid^29–31 and nonsmall cell lung cancers;³² additionally, a phase I clinical study demonstrated acceptable tolerance in patients with advanced malignancies,³³ and a phase II clinical trial is ongoing.³⁴ Though there are undesirable side effects associated with full agonist activity,³⁵ there exist PPARγ partial agonists endowed with reduced side effects.^36–41 For example, in the preclinical setting, PPARγ partial agonist balaglitazone displayed a better safety profile than full agonists.^34,42,43 Another partial agonist netoglitazone (MCC-555) has one-tenth the affinity to PPARγ as rosiglitazone, has lesser side effects,⁴⁴ and is significantly more potent.⁴⁵ Thus, the search for novel PPARγ partial agonists with structural diversity and safe biological profiles remains an attractive therapeutic strategy to circumvent cancer.

Recent reports suggested that combination treatment with HDAC inhibitors and PPARγ agonists increased cytotoxic effects in a synergistic/additive manner against various cancer cell lines, resulting in proliferation arrest and apoptosis. In some cases, even low doses of a PPARγ ligand in combination with a weak HDAC inhibitor resulted in more profound growth arrest than treatment with either drug alone.^46–48

On the basis of this literature, a series of 25 novel TZD-based naphthylidene derivatives were rationally designed and successfully synthesized in pursuit of a multitarget drug approach and simultaneous targeting of HDAC/PPARγ. Biological evaluation of compounds revealed their dual-targeting ability by partial transactivation of PPARγ and selective inhibition of HDAC4. To our knowledge, this is the first ever attempt to develop agents which simultaneously target HDACs and PPARγ, two highly desirable targets in cancer drug discovery. An investigation of the antiproliferative capacity of this series of compounds revealed uncompromised cytotoxicity in a panel of hematological and solid cancer cells, induction of apoptosis, and in vivo tumor regression in CCRF-CEM (T-cell leukemia) xenografts.

RESULTS AND DISCUSSION

Rationale of Designing PPARγ and HDAC Dual-Targeting Analogues.

The main challenge in designing dual HDAC inhibitors and PPARγ agonists was achieving a unique framework which satisfied the binding requirements of both targets. In our previous reports, a distinct pharmacophoric drug-design was used to individually achieve both classes of compounds.^49–53 Thus, on the basis of our experience with both targets, a multitargeting strategy was conceptualized in consideration of HDAC and PPARγ pharmacophore properties.

Traditional (full) PPARγ agonists consist of a hydrophobic tail linked to a central aryl ring, which is further linked through another small methylene bridge (linker 2) to the pharmacophoric TZD head (Figure 1). Examples are antidiabetic drugs pioglitazone and rosiglitazone. However, partial PPARγ agonists display a broader range of structural diversity, some being structurally similar to traditional agonists (e.g., netoglitazone), while others have an entirely different structural framework. The major distinguishing feature between full and partial PPARγ agonists is their binding pattern at the active site, which has been reviewed well in the literature. A key structural difference between partial agonist netoglitazone and traditional glitazones is the central naphthalene ring in place of a phenyl ring, suggesting a major contribution of naphthalene in shifting the molecule from full to partial agonist.

Figure 1. — Designing of (partial) PPARγ and HDAC dual targeting agents.

N-Substituted benzylidene TZDs (an aryl ring attached to TZD through –C═CH– instead of –CH–CH₂–), including our previously reported compounds and GQ-16, were found to be partial PPARγ agonists.⁵⁴ Both netoglitazone, with a naphthalene central aryl ring, and GQ-16, with a benzylidene TZD ring, have demonstrated antitumor potential.⁵⁵ Given the partial PPARγ transactivation and antitumor potential of these compounds, we sought to synthesize compounds with a naphthalene ring attached to TZD ring through a benzylidene like linker (–C═CH–)—thus generating the naphthylidene TZD derivatives which are evaluated herein (designed molecule, Figure 1).

Typical HDAC inhibitors share a broad pharmacophore with a surface recognition cap (SRC, denoted CAP herein) which binds with amino acids of the active site, a hydrophobic linker which occupies the active site channel, and a zinc binding group (ZBG) which chelates the catalytic zinc ion.⁵⁶ Previously, we developed HDAC inhibitors by placing a TZD ring centrally to obtain N-substituted TZD derivatives like P19 (Figure 1), or terminally to get naphthylidene TZDs like 3k (Figure 1) with good to moderate HDAC inhibitory activity.^50,52,53 Both TZD series showed different activity against HDAC4 and HDAC8, which are representative of class IIa and class I human zinc-dependent HDACs. While N-substituted TZD analogues were found to be inactive against HDAC4 with moderate activity against HDAC8 (e.g., P19 IC₅₀ = 9.3 μM), compound 3k with ortho-substituted naphthalene linker showed increased inhibitory activity on both HDAC4(IC₅₀ = 15 μM) and HDAC8 (IC₅₀ = 2.3 μM)⁵² (Figure 1). Despite significantly different chemical structures of P19 and 3k, their docked binding poses revealed that the carbonyl oxygen of carboxamide binds to the catalytic zinc ion and not the TZD ring. Thus, in the quest of modifying the structure of 3k series compounds to discover more potent HDAC inhibitors, we shifted substitutions at the naphthalene linker in the opposite ends to get a more extended shape than 3k. A primary docking study of these newly designed HDAC inhibitors at the active sites of HDAC4 and HDAC8 revealed that the TZD ring exhibited zinc binding interactions in HDAC4, whereas the carbonyl oxygen of carboxamide was bound to the zinc ion of HDAC8, which was a positive indication that the designed compounds could be HDAC inhibitors with differential potencies and selectivity. Similarly, HDAC inhibitors such as panobinostat have substitutions and a cyclic linker attached ZBG which are opposite to each other (Figure 1). We retained the naphthalene ring as a cyclic linker to help establish the structure–activity relationship (SAR) for HDAC inhibitory activity and partial PPARγ agonistic activity. Although compounds like 3k are structural isomers of the series described herein, the CAP portion have been varied to a great extent—aromatic, heterocyclic, and heteroaryl—to optimize for surface complementarity with HDAC active sites. In addition, the position of the substituents is such that it alters the shape of the molecules, thus orienting them differently from “series 3” and potentially leading to distinct HDAC selectivity and potency.

This rational designing led to oppositely substituted naphthylidene TZD structures in accordance with the pharmacophoric model of both targets (Figure 2). To clarify, the terminal aromatic/heterocyclic/heteroaromatic groups correspond to the lipophilic group of PPARγ agonists and to the CAP for HDAC8 inhibitors. Likewise, the carboxamide alkoxy moiety reflects linker 1 of PPARγ and the connecting unit between CAP and cyclic linker for HDAC4, while the carbonyl of this carboxamide may function as a ZBG for HDAC8. The naphthalene ring serves as the central aryl ring for PPARγ and as cyclic linker for HDACs. The methylene (–C═CH–) group corresponds to linker 2 for PPARγ and spacer for HDACs; and ultimately, the terminal TZD ring is a pharmacophore for PPARγ and ZBG for HDAC4. Therefore, we theorized that these compounds would have the capacity to simultaneously target HDACs and PPARγ.

Figure 2. — Fitting of designed dual PPARγ and HDAC targeting agents in typical pharmacophoric models of both targets.

Chemistry.

The procedures to synthesize the target compounds with a terminally substituted aromatic ring (7a–7l, 7o–7r, 7u–7v) were outlined in Scheme 1. Commercially available 6-hydroxy-2-naphthaldehyde (3) was reacted with 2,4-TZD (4) under Knoevenagel conditions to afford intermediate 5, which was further condensed with phenyl acetamides (2a–2l, 2o–2r, 2u–2v) under weakly basic conditions. Phenyl acetamides, in turn, were prepared from commercially available aromatic amines (1a–1l, 1o–1r, 1u–1v) as previously reported. Target compounds with a terminally substituted heterocyclic ring 7m, 7n, 7s, and 7t were synthesized using procedures as described in Scheme 2. The phenyl acetamides 2m, 2n, 2s, and 2t were condensed first with 3 and then were reacted by Knoevenagel conditions but using methoxy-ethanol as a solvent rather than traditional knoevenagel solvents. Use of methoxy-ethanol drastically improved the yield and purity of the final compounds. Target compounds 7w–7y were prepared as per the procedure detailed in Scheme 3 in a similar way to heterocyclic derivatives, with the variation of the solvent and reaction conditions.

Scheme 2. — ^aReagents and conditions: (a) chloroacetyl chloride, DCM/chloroform, TEA, stir, 0–5 °C, 1 h, rt, 8–12 h; (b) 6-hydroxy naphthaldehyde (3), DMF, K₂CO₃, stir 36 h; (c) 2,4-thiazolidinedione, methoxy ethanol, piperidine, reflux 3–4 h.

Scheme 3. — ^aReagents and conditions: (a) chloroacetyl chloride, chloroform, K₂CO₃, stir, 0–5 °C, 1 h, rt, 24–48 h; (b) 6-hydroxy naphthaldehyde (3), DMF, K₂CO₃, stir 48 h; (c) 2,4-thiazolidinedione, DMF, piperidine, reflux 3–4 h.

HDAC4/8 Activity Assay.

To determine the effects of synthesized derivatives 7a–7y (Figure 2) on the activity of HDACs and to detect if they exhibit selectivity against class I or class II, all 25 compounds were initially screened at 35 μM concentration on both isoforms, viz., HDAC4 from class II and HDAC8 from class I. The test compounds showed exceptional inhibitory effects on HDAC4, with markedly lower but significant activity on HDAC8 (Figure 3; Table S1 in Supporting Information). On the basis of the results gained in primary screening, compounds inducing a residual enzyme activity of <40% were evaluated at six concentrations to establish a dose–response curve (Figure 2, Table 1). Few compounds were found to be dual HDAC4 and HDAC8 inhibitors. Most of the compounds were more selective and potent on HDAC4 and at least 2 times potent on HDAC4 over HDAC8 at the tested concentrations. The best activities against HDAC4 were comparable to “Cpd 6”⁵⁷ (Table 1), indicative of the therapeutic potential of this compound series.

Figure 3. — Dose–response curves (DRCs) of indicated inhibitors (A–E) against HDAC4 and (F–H) against HDAC8. Residual enzyme activity of HDAC4 or HDAC8 for compounds **7a–7m** (I) and compounds **7n–7y** (J) in the presence of 35 μM of the indicated compounds. Data represent means and standard deviations, n = 3. Compounds with less than 40% residual enzyme activity were taken further to determine IC₅₀ values.

Table 1.

IC₅₀ Values of the “Series 7” against HDAC4 and HDAC8 ^a


compound	Ar group	HDAC4 IC₅₀ (μM)	HDAC8 IC₅₀ (μM)
7a	phenyl	2.1 ± 0.3	4.5 ± 0.2
7b	4-fluorophenyl	1.6 ± 0.3	6.6 ± 0.2
7c	4-methylphenyl	1.7 ± 0.3	9.0 ± 0.2
7d	4-methoxyphenyl	4.7 ± 0.1	>50
7e	3-trifluoromethylphenyl	2.5 ± 0.4	>50
7f	3-chlorophenyl	3.8 ± 0.1	>50
7g	3-methoxyphenyl	1.6 ± 0.2	7.6 ± 0.2
7h	3,4-dichlorophenyl	5.5 ± 0.3	>50
7i	2-bromo-4,6-difluorophenyl	1.1 ± 1.7	>50
7j	2-phenoxyphenyl	5.2 ± 0.5	>50
7k	2,4-difluorophenyl	3.9 ± 0.1	>50
7l	4-bromo-2-methylphenyl	0.55 ± 0.05	7.4 ± 0.3
7m	pyridin-2-yl	17 ± 0.7	>50
7n	6-methylpyridin-2-yl	1.1 ± 1.2	7.5 ± 0.2
7o	4-Br phenyl	2.9 ± 0.1	16 ± 0.5
7p	3-chloro-5 (trifluoromethyl)phenyl	4.0 ± 0.2	>50
7q	4-nitrophenyl	1.7 ± 0.4	4.0 ± 0.2
7r	4-bromo-2-fluorophenyl	1.9 ± 0.1	>50
7s	6-fluoropyridin-2-yl	0.84 ± 0.22	7.2 ± 0.2
7t	5-methylisoxazol-3-yl	1.7 ± 0.8	>50
7u	3-chloro-4-methylphenyl	1.1 ± 0.4	>50
7v	3,4-dibromophenyl	4.9 ± 0.3	>50
7w	benzo[d]thiazol-2-yl	0.42 ± 0.05	2.7 ± 0.2
7x	4-methylbenzo[d]thiazol-2-yl	1.2 ± 0.4	5.8 ± 0.1
7y	6-ethoxybenzo[d]thiazol-2-yl	3.6 ± 0.3	17 ± 0.3
Cpd 6 ⁵⁷	-	0.22	>50
PCI-34051 ⁵⁹	-	10	0.024

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Data represent mean ± sd (standard deviations), n = 3. Compounds with less than 40% residual enzyme activity were taken further to determine IC₅₀ values.

Against HDAC8, 12 out of 25 compounds possessed inhibition capacity. The remaining compounds showed no or only moderate activity at tested concentrations. Compounds 7a, 7b, 7c, 7g, 7l, 7n, 7q, 7s, 7w, and 7x exhibited IC₅₀ values of <10 μM, 7o and 7y of < 20 μM. The most potent inhibitor was 7w, which had an IC₅₀ = 2.7 ± 0.2 μM. Among the compounds with a substituted aromatic group (Ar), it was observed that the unsubstituted (7a), monohalo-substituted with F or Br (7b, 7o), and monoalkyl substituted (7c) derivatives retained HDAC8 inhibitory activity. Compounds 7d and 7g are structural isomers with p-OCH₃ and m-OCH₃ respectively, but only 7g exhibited inhibitory potential, indicating that the point of methoxy group attachment may be important. Compounds with dihalo substitution (7h, 7i, 7k, 7r) were found to be inactive, thus suggesting that dihalo substitution leads to loss of HDAC8 inhibition. Likewise, substitution with Cl (7f), CF₃ (7e) or disubstitution with these two groups (7p) did not show HDAC8 inhibition. Additionally, it was observed that compounds with disubstitution at position 3- and 4- of the phenyl ring (7h, 7u, 7v) were not active. When the Ar group is a heterocyclic ring such as pyridinyl, halo-substituted pyridinyl (7s) and methyl substituted pyridinyl (7n) derivatives displayed greater HDAC8 inhibition than the unsubstituted compound (7m). Comparison between benzothiazole containing compounds revealed that an unsubstituted benzothiazole (7w) ring was preferred over alkyl (7x) and alkoxy substitution (7y).

As far as HDAC4 inhibitory activity is concerned, all derivatives exhibited HDAC4 inhibition with IC₅₀ < 6.0 μM, except 7m which had IC₅₀ = 17 ± 0.7 μM. The most potent compounds exhibiting IC₅₀ values in the submicromolar range were 7l, 7s, and 7w (IC₅₀ = 0.55 ± 0.05 μM, 0.84 ± 0.22 μM, and 0.42 ± 0.05 μM respectively). Among aromatic analogues (Ar = substituted phenyl) compounds with no substitution (7a), monohalo-substitution (7b, 7f, 7o), monoalkyl substitution (7c), and monoalkoxy substitution (7d, 7g) were found to be more potent than dihalo substituted compounds (7h, 7k, 7v except 7r). Even, disubstitution with a halogen and methyl group (7l, 7u) was well tolerated with significant activity. In the case of pyridinyl and benzothiazolyl derivatives, the effect of substitution pattern on inhibitory activity was found similar to that of HDAC8. Among pyridinyl derivatives, halogen substitution (7s) and alkyl substitution (7n) led to more potent activity than an unsubstituted pyridine ring (7m), whereas in benzothiazole containing compounds, an unsubstituted benzothiazole ring (7w) was preferred over alkyl (7x) and alkoxy substitution (7y). Since all compounds exhibited HDAC4 inhibition, it can be assumed that an Ar group of all three types, viz., aromatic, heterocyclic, and heteroaromatic, is well tolerated with significant retention of activity.

Compounds 7d, 7e, 7f, 7h, 7i, 7j, 7k, 7m, 7p, 7r, 7t, 7u, and 7v were found more potent on HDAC4 over HDAC8, whereas compounds 7a, 7b, 7c, 7g, 7l, 7n, 7o, 7q, 7s, 7w, 7x, and 7y were found to be dual inhibitors of HDAC4 and HDAC8 with at least 2 times more potency (as reflected from IC₅₀ values) toward HDAC4 than HDAC8.

The difference between our previously reported “series 3” and the current “series 7” is only the position of the TZD ring on the central naphthalene ring. Thus, shifting the point of TZD ring attachment to the opposite side on naphthalene ring leads to an extreme change in HDAC potency and selectivity. In the previously reported “series 3”, the arrangement of the various groups in the molecule was such that they adopted an L-shape which is an ideal fit at the active site of HDAC8 as per the Hou et al. model; instead, in our current “series 7”, the shifting of the TZD ring to the opposite site causes the structure to deviate from an L-shape, which could be the reason why the current series are less selective and potent inhibitors of HDAC8.⁵⁸ Nevertheless, the common element between our previously reported “series 3” and current “series 7” is the naphthalene linker, thus supporting our hypothesis of incorporating a naphthalene ring as cyclic linker to obtain potent HDAC inhibitors.

Molecular Docking into HDAC4 and HDAC8.

Different TZD scaffolds show different activities against HDAC4 and HDAC8, which are representatives of class IIa and class I of human zinc-dependent HDACs. While N-substituted TZD analogues are generally inactive against HDAC4, there are some examples with moderate activity against HDAC8 (e.g., P19 with an IC₅₀ value of 9.3 μM,⁵³ Figure 4). Docking results suggested that P19 binds to the catalytic zinc ion through its carbonyl oxygen and occupies the lower side pocket which connects the canonic active site pocket and acetate release channel.

TZD analogue 3k with ortho-substituted naphthalene linker showed increased inhibitory activity on both HDAC4 and HDAC8⁵² (Figure 4). Despite their different chemical structures, in spacer and substitution pattern at the TZD group, P19 and 3k have similar features in their docked binding poses. Namely, the protrusion of the aromatic carboxamide moiety into the transition area between active site and acetate release channel and binding of the carbonyl oxygen to the catalytic zinc ion. “Series 7” differentiate from the branched 3k in that the substitutions at the naphthalene linker are in the opposite position from the TZD group, thus forming a more extended shape. This difference led to a tremendous increase in activity against both HDAC isoenzymes (Figure 4). Compound 7w also showed low micromolar activity against HDAC8 and HDAC4, thus resulting in a dual HDAC4/8 inhibitor with some preference for HDAC4.

To rationalize the observed dual activity of “series 7” analogues against HDAC8 and particularly HDAC4, a comprehensive docking study was performed. At first, the docking routine was validated by redocking of the respective ligands into the used crystal structures of HDAC8- (PDB ID: 3SFF) and HDAC4-ligand complexes (PDB IDs: 2VQJ and 4CBY). The docked and crystallized poses of the ligand within the binding pocket of HDAC8 (PDBID: 3SFF) showed excellent overlap with an RMSD over 26 heavy atoms of 0.2 Å. The thiophene linker and trifluoromethyl warhead of the redocked ligand in HDAC4 (PDB ID: 2VQJ) show a good RMSD (root-mean-square deviation) value of 0.4 Å with respect to the crystal structure (Table S1 in Supporting Information). Since the aromatic headgroup of the trifluoromethyl ketone ligand protrudes into free solution, this part of the molecules is intrinsically flexible and thus not considered for the calculation of RMSD. For HDAC8, the crystal structure with PDB-ID 3SFF, which was previously utilized in docking of 3k, was selected.⁵² All compounds of “series 7” superposed well and docked smoothly into the binding pocket of HDAC8, showing a very similar binding mode to 3k (Tables S2, S3 in Supporting Information). The aromatic ring of the carboxamide group of 7l fit perfectly into the lower binding pocket adjacent to the catalytic center at the entrance of the acetate release channel, and the carbonyl oxygen was bound to the catalytic zinc ion (Figure 5A). Moreover, the naphthalene linker forms a π-stacking interaction with Phe152 and Phe208 and a π-sulfur interaction with Met274 (Figure 5A,B).

Figure 5. — (A) 3D docking pose of 7l within HDAC8, (B) 2D interactions between 7l and HDAC8. (C) Docked 3D binding pose of 7l within the enlarged binding groove of HDAC4_o. (D) 2D interactions between 7l and HDAC4_o. Conventional hydrogen bonds are indicated by dotted green lines, alkyl and π-alkyl interactions by dotted magenta or pink lines. A dotted gray line denotes metal binding, whereas a dotted orange line highlights a π-sulfur interaction.

The TZD group points out of the binding pocket and is exposed to the outer solvent. The malleability of the HDAC8 binding pocket allows for accommodation of the branched TZD-analogue 3k as well as the more linearly shaped 7l. This exceptional flexibility of HDAC8 has been exploited previously for the design of linkerless or branched isoenzyme selective inhibitors.^60,61 However, all of these active compounds contain the potentially problematic hydroxamate group of most canonical HDAC inhibitors. Overall, compounds of “series 7” show good docking scores that are similar to or better than 3k (Table 2).

Table 2.

GBVI/WSA dG Docking Scores for Indicated Molecules and HDAC Isoenzymes

ID	HDAC4_o	HDAC8	ID	HDAC4_o	HDAC8
7a	−8.7	−9.0	7n	−9.2	−9.6
7b	−8.7	−8.8	7o	−9.7	−9.8
7c	−9.1	−9.8	7p	−9.0	−10.2
7d	−9.3	−10.3	7q	−10.3	−9.9
7e	−8.9	−10.0	7r	−9.9	−10.2
7f	−9.1	−9.9	7s	−8.2	−10.7
7g	−10.3	−9.9	7t	−9.5	−10.5
7h	−9.1	−9.8	7u	−8.5	−10.0
7i	−9.4	−9.7	7v	−8.9	−10.2
7j	−10.5	−10.1	7w	−9.6	−10.2
7k	−9.0	−9.8	7x	−9.6	−10.3
7l	−9.4	−10.2	7y	−10.5	−11.2
7m	−9.2	−9.1	3k	−8.7	−9.5*

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To understand the difference between 3k and 7l in molecular recognition of HDAC4 and HDAC8 appears more complex and challenging. It is of utmost importance to recollect that different types of inhibitors have been shown to stabilize either the open or the closed conformation of the catalytic domain of HDAC4 because of its conformationally flexible second zinc-binding domain.^62,63 To explore the impact of open (PDB ID: 2VQJ) and closed (PDB ID: 4CBY) conformations of HDAC4 on the binding affinity of the most active analogues, 7l and 7w (IC₅₀ 0.55 ± 0.05 and 0.42 ± 0.05 μM, respectively), docking was performed using both crystal structures. Binding to the enlarged pocket of open conformation HDAC4 (HDAC4_o) yielded more favorable binding energies than closed HDAC4 (HDAC_c) (Table S2 in Supporting Information). Consequently, all TZD analogues have been docked into the large binding groove of HDAC4_o, yielding good scores and indicating favorable contacts between protein and ligand (Table 2). A comparison with 3k reveals that the compounds of “series 7” exhibit favorable interactions with both HDAC4_o and HDAC8, while 3k shows good affinity toward HDAC8 but is poorly recognized by HDAC4_o.⁵² Thus, docking results are in good agreement with experimental data and may provide insight into important contacts that determine binding mode of action with HDAC4. Docking suggested that “series 7” analogues bind to HDAC4_o rather than HDAC4_c. The enlarged binding groove of HDAC4_o is complementary to the linear shape of the TZD analogues of “series 7”, offering favorable contacts between the amino acids at the surface of the binding pocket and the ligands (Figure 5C). The resulting binding poses were similar among all analogues (Figure S1A,B in Supporting Information). In contrast to the binding mode of the TZD analogues in HDAC8, which is determined by an interaction between the catalytic zinc ion and carbonyl oxygen of the ligand, “series 7” compounds bind the corresponding zinc ion through the TZD group in HDAC4_o (Figure 5C,D). A closer look at the distinct contacts between 7l and HDAC4_o revealed multiple interactions between the TZD group and binding pocket: one carbonyl oxygen of the TZD ring interacts with the catalytic zinc ion, the amide nitrogen serves as hydrogen donor for His159, and the sulfur atom forms a π-sulfur interaction with the aromatic ring of Phe168 (Figure 5C,D). Moreover, the naphthalene linker is supposed to undergo hydrophobic interactions with Pro156. Two additional charge enhanced hydrogen bonds, between theoxygen next to the naphthalene moiety and Arg154 as well as the distal carbonyl oxygen and Lys20, contribute significantly to the binding of 7l to HDAC4_o (Figure 5C,D). Possible hydrophobic interactions between neighboring Arg37, Arg154, and the aromatic head group may also increase affinity depending on the substitution pattern. Altogether, the experimentally demonstrated dual activity of TZD compounds from “series 7” against HDAC4 and HDAC8 agrees with favorable docking scores for both HDAC isoenzymes. Furthermore, the docking results suggest two distinct binding modes of 7l and analogues to HDAC8 and the open conformation of HDAC4 characterized by different complexation of the catalytic zinc ion.

PPARγ Transactivation Assay.

Compounds 7a–7y were analyzed via PPARγ-GAL4 transactivation assay on HepG2 cells in agonist mode at 25, 5, and 1 μM concentrations. Rosiglitazone at a 2 μM concentration was used as a control, while the blank contained 0.1% dimethyl sulfoxide (DMSO). Compounds 7i, 7l, and 7r were the most active and showed efficacy of 20–30% followed by 7c, 7o, and 7q with an efficacy around 10% compared with the control (Table 3) (Figure S4 in Supporting Information). Many compounds showed partial activation of PPARγ, but because E_max was less than 10%, their activity was considered negligible. However, we were successful to determine EC₅₀ (half maximal effective concentration) values for the six compounds listed in Table 3. Thus, our hypothesized design of naphthylidene TZD analogues as partial PPARγ agonists was successful. The most potent partial agonists were 7i and 7l with EC₅₀ values of 0.245 ± 0.006 and 0.359 ± 0.031 μM, respectively. In spite of the small number of PPARγ active compounds, some preliminary remarks can be made about structure–activity relationships. It is very interesting to note that five p-Br (bromo) substituted compounds, 7i, 7l, 7o, 7r, and 7v, displayed PPARγ activity, which indicates that this substitution has the appropriate requisites to elicit the transactivation capacity of these derivatives. For these compounds, other substituents can be tolerated at the ortho position, particularly fluorine (7i, 7r) or methyl (7l), whereas a methyl or a polar nitro group alone at the para position of the phenyl ring led to less potent derivatives (7c, 7q). In contrast, the presence of two bromine atoms, as in the 3,4-disubstituted derivative 7v, led to poor activity. This suggests that an excess steric bulk in this part of the molecule is detrimental for the interaction with the receptor. Given that all heterocyclic and pyridinyl derivatives showed very low activity, it can be assumed that the phenyl ring is more appropriate to achieve significant PPARγ transactivation.

Table 3.

PPARγ Transactivation Assay ^a


	PPARγ
compound	E_max%^b	EC₅₀ μM	“Ar” group
7c	13 ± 2	1.220 ± 0.260	4-methylphenyl
7i	22.4 ± 1.8	0.245 ± 0.006	2-bromo-4,6-difluorophenyl
7l	32 ± 3	0.359 ± 0.031	4-bromo-2-methylphenyl
7o	13.0 ± 0.2	0.729 ± 0.027	4-bromophenyl
7r	27 ± 6	0.791 ± 0.025	4-bromo-2-fluorophenyl
7q	8.5 ± 1.5	1.610 ± 0.280	4-nitrophenyl

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EC₅₀ values with mean ± SD.

Efficacy values (E_max) were calculated as a percentage of the maximum obtained fold induction with the reference compounds. All transfection experiments were repeated at least twice in triplicate.

These findings illustrate the potential of 7i, 7q, and 7r as dual targeting partial PPARγ agonist and selective HDAC4 inhibitor compounds, and of 7c, 7l, and 7o to target PPARγ, HDAC4, and HDAC8 but with more efficacy (3- to 10-fold) on HDAC4.

Molecular Docking into PPARγ.

To understand the structural basis for the observed partial agonism of 7i, 7l, 7o, 7r, 7c, 7q toward PPARγ, we undertook docking simulations using the Glide module, which is part of the Maestro software suite. Docking experiments were carried out into the X-ray crystal structures of PPARγ ligand binding domain (LBD) complexed to partial agonist CAY10638 (PDB ID: 6DGR).⁶⁴ This structure was chosen as a template because of the good resolution (2.15 Å) and the similarity of the cocrystallized ligand with the candidate compounds, both containing a TZD headgroup and an unsaturated linker, which restricts the mobility of the TZD group. Analysis of the CAY10638/PPARγ complex revealed that the ligand is H-bonded via two crystallographically observed water molecules to the protein: via HOH708 to L340 (β-sheet) and via HOH706 to S342 (β-sheet). Accordingly, the two water molecules were included in the docking experiments.

The LBD of PPARγ consists of a hydrophobic entrance (arm III) that branches off into two subsites: the polar arm I, which is extended toward H12, and the hydrophobic arm II, which is located between helix H3 and β-sheet.

Compound 7i fit well within the PPARγ LBD, adopting a U-shaped conformation like the known full agonist Rosiglitazone. The interactions between 7i and the PPARγ LBD involved many H-bonds, one halogen bond, and several hydrophobic interactions (Figure 6A,B). The TZD headgroup is located in arm I and establishes a bifurcated H-bond with N^ε atom of H323 (d = 2.8 Å) and Oγ atom of S289 (d = 3.2 Å) by one of two carbonyl oxygens. Unlike full agonist Rosiglitazone, 7i shows no direct H-bond with residue Y473 in the activation function domain (AF-2) located on H12. Interestingly, the superimposition of 7i on the cocrystal structure of Rosiglitazone bound to PPARγ LBD (PDB ID: 4EMA) revealed that the TZD headgroup of 7i undergoes a slight shift toward H3, thus preventing the formation of a key H-bond with residue Y473 (Figure 6C). Because stabilization of the AF2 helix in the activated conformation is a key characteristic of full agonism,⁶⁵ the lack of direct interaction between this domain of the receptor and 7i may explain the observed partial agonist/modulator activities of this class of compounds. The naphthalene moiety is placed in the center of the LBD and makes hydrophobic interactions with C285, I326, Y327, L330, F363, and M364. The phenyl amide tail lies in the subpocket between H3, β-sheet, and Ω-loop (β-sheet subpocket), establishing numerous nonpolar and polar interactions with the participation of HOH708 and HOH706 in setting-up an indirect H-bond network. Specifically, the oxygen atom bound to the naphthalene moiety makes an H-bond with HOH708 (d = 3.1 Å), which in turn interacts with the C═O backbone of L340 (d = 3.1 Å). The bromine atom in the ortho position of the phenyl ring forms a halogen bond with the structural water HOH706 (d = 3.1 Å), that in turn interacts with the NH backbone of S342 (d = 3.1 Å). Hydrophobic contacts are also observed between 7i and the subpocket residues V339, I341, M348 (β-sheet); I281 (H3); and F264 (Ω-loop). These interactions contribute to the stabilization of the H3/β-sheet/Ω-loop region of the LBD, similar to other PPARγ partial agonists such as BVT.13, MRL-24, and nTZDpa.⁶⁶ It has in fact been demonstrated that the activity of partial agonists, which do not robustly stabilize H12, may stem from the stabilization of the β-sheet subpocket.^66–69 In addition, the terminal phenyl ring appears to be optimally oriented for a favorable edge-to-face π-stacking interaction with H266 on the Ω-loop, which contributes to further increase the Ω-loop stabilization. It is thus conceivable to suggest that ligands of PPARγ can afford graded transcriptional responses by employing a compensatory mechanism of β-sheet subpocket interactions to balance the lack of H12 stabilization. However, it is important to note that the Ω-loop is highly unstable and the residues within this loop are quite flexible; thus, the prediction of ligand/Ω-loop interactions might not be accurate and must be interpreted accordingly.^67,70

Figure 6. — In silico docking of compound 7i into the PPARγ binding pocket. (A) Binding mode of compound 7i (partial agonist, green sticks) into the PPARγ binding site represented as a gray ribbon model. Only amino acids located within 4 Å of the bound ligand are displayed (white sticks) and labeled. H12 is shown in slate. H-bonds discussed in the text are depicted as dashed yellow lines. The halogen bond is shown as dashed magenta lines. The water molecules bridging the interaction of the ligand with the protein are displayed as red spheres. (B) 2D ligand-interaction diagram of 7i. The plot was generated by LigPlot+. H-bonds are shown as dashed yellow lines, while the halogen bond is shown as dashed magenta lines. The water molecules are displayed as red spheres. The spoked arcs represent residues making nonbonded contacts with the ligand. (C) Cα superposition of the complexes of PPARγ with compound 7i and Rosiglitazone (full agonist, magenta sticks, PDB ID: 4EMA).

Docking of 7l, which has a similar potency toward PPARγ as 7i, revealed a binding mode of this compound comparable to that described above for 7i, with the only consistent difference being the lack of the halogen bond, which is outweighed by the formation of a H-bond between the carbonyl oxygen of the phenylacetamide tail and HOH706 (3.5 Å), that in turn interacts with the C═O backbone of S342 (d = 3.1 Å). Moreover, the methyl group at the ortho position on the terminal phenyl ring allows 7l to form additional hydrophobic interaction with L353.

Further docking studies of 7o, 7r, 7c, 7q revealed that these compounds were in the same position as 7i and 7l but were unable to strongly stabilize the β-sheet, thus showing a decrease in potency (Figure S5 in Supporting Information). The low efficacy is due to the lack of the halogen bond with HOH706, since bromine is placed in para position in 7o and 7r, and to steric clashes of methyl and nitro group in 7c and 7q, respectively, with H266 and F264 residues belonging to the Ω-loop.

Cytotoxicity Assessment by DNS Assay.

On the basis of the prior experiments, it was discovered that derivatives 7c, 7i, 7l, 7o, 7r, and 7q were dual HDAC and PPARγ targeting agents; hence, they were considered for further evaluation in regard to their antitumor activity. Compounds 7e, 7f, and 7j were also selected as they were selective for HDAC4, as was 7g for its dual activity against HDAC4 and HDAC8. Thus, a total of 10 compounds were screened via differential nuclear staining (DNS) assay to assess their cytotoxic potential against a panel of seven cell lines. The panel consisted of solid tumor cells: HeLa (cervical adenocarcinoma, epithelial), MDA-MB-231 (triple negative breast, epithelial), and SH-SY5Y (neuroblastoma, epithelial); hematological tumor cells: CCRF-CEM (T-cell leukemia), Ramos (Burkitt’s B-cell lymphoma), and HL60 promyelocytic leukemia, myeloblasts); and noncancerous cells: HS-27 (normal foreskin, fibroblasts). A primary single dose screening of all 10 compounds was performed at a concentration of 10 μM, and those which elicited greater than 40% cell death (Table 4) were analyzed at several concentrations to find their half maximal cytotoxic concentration (CC₅₀). CC₅₀ values indicate the average concentration of compound required to kill 50% of the sample population and is reported as mean ± SD in Table 5.

Table 4.

Primary Single Dose DNS Screening of Selected Compounds for Cytotoxicity in a Panel of Seven Cell Lines at 10 μM Concentration ^a

	% cell death at 10 μM
compound	CEM	Ramos	HL60	HeLa	MDA-MB-231	SH-SY5Y	HS-27
7c	>40	>40	20.95	>40	22.80	>40	13
7e	25.87	>40	19.55	39.09	5.96	0	>40
7f	>40	>40	27.58	29.68	2.84	10.79	22.56
7g	>40	>40	0	>40	>40	0	24.69
7i	>40	>40	12.43	>40	>40	>40	>40
7j	40.24	>40	0	>40	>40	>40	0
7l	30.82	29.78	32.90	>40	31	>40	24.90
7o	37.44	34.53	17.64	>40	0	>40	0
7q	42.28	35.18	12.34	38.95	>40	0	15.32
7r	>40	3.91	0	0	0	>40	>40

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CEM: T cell leukemia, Ramos: Burkitt’s B cell lymphoma, HL60: promyelocytic leukemia (myeloblasts), HeLa: cervical adenocarcinoma (epithelial), MDA-MB-231: triple negative breast (epithelial), SH-SY5Y: neuroblastoma (epithelial), HS-27: normal foreskin (fibroblasts).

Table 5.

CC₅₀ Values of Selected Compounds (7c, 7e, 7f, 7g, 7i, 7j, 7l, 7o, 7q, 7r) and Standard Drugs (SAHA, Pioglitazone) ^a

compounds	cell line	CC₅₀ (μM)	SCI
7c	CEM	2.8 ± 0.31	14.4
	Ramos	7.0 ± 1.17	5.8
	HeLa	10.3 ± 0.56	3.9
	SH-SY5Y	49.5 ± 1.09	0.8
	HS-27	40.2 ± 4.75	-
7e	Ramos	6.2 ± 0.28	>10
7f	CEM	10.6 ± 0.22	>10
	Ramos	9.1 ± 0.08	>10
7g	CEM	10.7 ± 0.41	>10
	Ramos	9.3 ± 0.01	>10
	HeLa	10.4 ± 0.58	>10
	MDA-MB-231	9.8 ± 0.22	>10
7i	CEM	9.6 ± 0.15	4.2
	Ramos	9.6 ± 0.14	4.2
	HeLa	10.4 ± 0.16	3.8
	MDA-MB-231	9.8 ± 0.1	4.1
	SH-SY5Y	21.8 ± 0.41	1.8
	HS-27	39.9 ± 1.95	-
7j	Ramos	10.0 ± 0.39	>10
	HeLa	10.2 ± 0.52	>10
	MDA-MB-231	10.3 ± 0.12	>10
	SH-SY5Y	52.3 ± 3.09	>10
7l	HeLa	9.9 ± 0.25	>10
	SH-SY5Y	91.1 ± 4.26	>10
7o	HeLa	10.1 ± 0.04	>10
7q	MDA-MB-231	55.8 ± 1.56	>10
7r	CEM	40.9 ± 3.16	1.4
	SH-SY5Y	16.0 ± 0.69	3.6
	HS-27	57.0 ± 8.45	-
Pioglitazone	CEM	0% @ 50 μM	-
	HeLa	0% @ 10 μM	-
SAHA	CEM	2.5 ± 0.13	-
	HeLa	2.8 ± 1.47	-

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CC₅₀ reported as average concentration ± std. deviation (μM); SCI = CC_50HS‑27/CC_50cancer; Nd*-Not determined

Several experimental compounds were cytotoxic at <10.0 μM (Table 5) on nearly all cancer cell lines except SH-SY5Y; however, compounds 7c and 7i were identified as the most potent candidates from this series. The greatest potency of compound 7c was against CEM (CC₅₀ = 2.8 μM), Ramos (CC₅₀ = 7.0 μM), and HeLa (CC₅₀ = 10.3 μM), whereas 7i was active against CEM (CC₅₀ = 9.6 μM), Ramos (CC₅₀ = 9.6 μM), and MDA-MB-231 (CC₅₀ = 9.8 μM). In comparing the cytotoxicity of “series 7” compounds with existing HDAC or PPARγ-targeted therapeutics, class I and II HDAC inhibitor suberoylanilide hydroxamic acid (SAHA; CEM CC₅₀ = 2.5 μM and HeLa CC₅₀ = 2.8 μM) displayed similar potency to 7c, and highly selective PPARγ agonist pioglitazone had no cytotoxic effect even at 50 μM. Dose–response curves (DRCs) for compounds 7c and 7i against the CEM cell line are shown in Figure 7.

Figure 7. — Dose–response curves of compounds 7c and 7i toward CCRF-CEM; n = 3.

Compounds 7c and 7i Exhibit Selectivity toward Tumorigenic Cells.

To compare the cytotoxicity of compounds 7c and 7i between tumorigenic and normal cells, the CC₅₀ value for each compound against HS-27 cells was divided by the CC₅₀ of each cancer cell line to generate selective cytotoxicity index (SCI) values. SCI values greater than 1.0 denote the ability of a given compound to kill cancer cells more effectively than cells of noncancerous origin.

These results revealed substantial selectivity of experimental compounds 7c and 7i toward CEM and other cancer cell lines within our panel. Compound 7c was the most selective, with a 14.4 SCI in the CEM cell line, whereas compound 7i had an SCI value of 4.2. Additional selectivity values for these compounds (and others) are presented in Table 5. Based on the potency and selectivity of 7c and 7i, CEM cells were the chosen model for several experiments that are described herein.

Apoptosis Assay.

To determine whether cell death elicited by experimental compounds 7c and 7i was occurring via apoptosis or necrosis, an Annexin V-fluorescein isothiocyanate/propidium iodide (AnnexinV-FITC/PI) assay was performed via flow cytometry. In this experiment, CEM cells were treated in triplicate with the CC₅₀ or 2xCC₅₀ of 7c, 7i, or SAHA (for comparison) and incubated for 72 h. 4% DMSO (dimethyl sulfoxide), 1 mM H₂O₂(hydrogen peroxide), and untreated cells were utilized as vehicle, positive, and negative controls respectively (Figure S6 in Supporting Information). Phosphatidylserine (PS) is a phospholipid which flips from the inner to the outer leaflet of the plasma membrane and serves as an “eat me” signal in apoptotic cells. Annexin V is a cellular protein with high affinity for PS that is commonly conjugated to the fluorochrome FITC and used as a probe for PS translocation. Propidium iodide, however, is permeable to all cells with compromised membranes. Apoptotic cell populations in this assay are those which stain positive for AnnexinV-FITC, whereas necrotic cells are those which stain positively for PI but negative for AnnexinV-FITC. This analysis identified significant PS externalization in 7c (21.46 ± 0.33%; p < 0.001) and 7i (26.53 ± 0.96%; p < 0.001) CC₅₀-treated samples when compared with the vehicle control, implying the stimulation of apoptosis by these compounds (Figure 8). Dose (CC₅₀ vs 2×CC₅₀) displayed negligible effect on the proportion of apoptotic cells. Approximately 40 000 events (cells) were analyzed per sample, and statistical significance was determined by Student’s t test (Tables S3–S6 in Supporting Information).

Figure 8. — AnnexinV-FITC/PI Assay in CCRF-CEM after 72 h exposure to **7c, 7i**, and controls (SAHA, H₂O₂); n = 3, ***p < 0.001.

Cell Cycle Analysis.

To evaluate the effect of 7c and 7i on the cell cycle, flow cytometry was used to quantify DNA content within each cell sample. CEM cells were exposed, in triplicate, to the CC₅₀ or 2×CC₅₀ of each compound for 72 h. HDAC inhibitor SAHA was likewise included for comparison. 4% v/v DMSO, 1 mM H₂O₂, and untreated cells were utilized as vehicle, positive, and negative controls repectively. After the incubation period, cells were collected and resuspended in a nuclear isolation medium containing DNA-intercalating dye DAPI (NIM-DAPI) immediately prior to analysis. DAPI fluorescent signal was used to quantify the replication status of cells within each sample, as its intensity is directly proportional to the amount of DNA. Approximately 40 000 events (cells) were analyzed per sample, and statistical significance was determined by Student’s t test (Tables S7–S9 in Supporting Information).

DNA fragmentation, represented by the sub-G0/G1 population, is a key feature of apoptosis. Despite significant apoptosis in our AnnexinV-FITC/PI assay at the same time point (Figure 8), just 6% of sub-G0/G1 accumulation was evident after treatment with 7c and 7i at either concentration. Compound 7c did not have a significant effect on the cell cycle, whereas G0/G1 arrest (p = 0.0103) was evident in 7i CC₅₀-treated samples. Thus, identifying a distinct effect of each compound on the cell cycle which also differs from SAHA (Figure 9).

Figure 9. — Cell cycle distributions in CCRF-CEM after 72 h exposure to **7c, 7i**, and control SAHA (A). Graphical representation of distribution of the cells treated with 7c, untreated control, DMSO, H₂O₂, and SAHA (B). Graphical representation of distribution of the cells treated with 7i untreated control, DMSO, H₂O₂, and SAHA. Histograms of vehicle (C), compound 7i (D), compound 7c (E); n = 3, *p < 0.05, **p < 0.01, ***p < 0.001.

Western Blotting.

The c-Myc oncogene is known as a master controller of tumor cell growth regulation and metabolism, which are closely inter-related.⁷¹ The metabolic changes driven by c-Myc overexpression, which occurs often in tumor cells, are essential to support the synthesis of nucleic acids, and various proteins/lipids necessary for rapid cell proliferation.⁷² Thus, downregulation of the c-Myc gene could help to control proliferation of tumor cells. Treatment with both PPARγ agonists and HDAC inhibitors have shown to decrease expression of c-Myc. The PPARγ agonist class glitazones, which include insulin-sensitizing drugs like pioglitazone, have demonstrated an ability to downregulate this gene in various cancer cells.⁷³ When treated with HDAC inhibitor SAHA, c-Myc is acetylated at L-323, and its expression decreases, leading to TRAIL activation and apoptosis.⁷⁴ Thus, downregulation of c-Myc is an important aspect of antiproliferative effects exerted by these classes of compounds. Often, c-Myc is activated in different types of leukemia and plays a vital role in the induction and progression of leukemogenesis.^75–78 To ascertain the effects of PPARγ and HDAC dual targeting compound 7c in CEM (T-cell leukemia) cells, immunoblotting was performed. Western blot analysis of compound 7c in CEM cells revealed downregulation of the c-Myc protein much greater than positive control pioglitazone (Figure 10). To assess if the observed suppression of c-Myc was a cascading effect associated with upregulation of tumor suppressor gene p53,⁷⁹ this protein was also evaluated; however, no upregulated expression was observed with exposure to compound 7c. This p53-independence suggests that c-Myc suppression could be a feature of the dual HDAC inhibition and PPARγ agonism exerted by compound 7c.

Figure 10. — Western blotting of CEM cells incubated with compound 7c (10 μM) and positive control, pioglitazone (10 μM), and untreated cells (UT) for 5 h; n = 2, *p < 0.05, **p < 0.0001. The graph shows the normalized data with respect to TBP band.

Caspases are also known as key mediators of apoptosis,⁸⁰ and among them, caspase-3 is a frequently activated death protease, which catalyzes the cleavage of many important cellular proteins leading to cell death.⁸¹ Both HDAC inhibitors (like SAHA) and PPARγ agonists (like pioglitazone) are linked to enhanced expression of cleaved caspases and apoptotic cell death.^82–84 In agreement with these observations, Western blotting revealed an increased expression of cleaved caspase-3 with compound 7c treatment compared with positive control pioglitazone (Figure 10).

The compounds of “series 7” are the very first evidence of molecules simultaneously targeting HDAC and PPARγ. The overall aim of these experiments was an initial evaluation of the antitumor potential of this unique class of molecules. Several analogues, particularly compound 7c, demonstrated effective antitumor activity at micromolar concentrations and substantial selective cytotoxicity. Though further analyses are needed to fully elucidate their mechanism of action, preliminary data on “series 7” strongly supports apoptotic cell death. This is evident by the translocation of PS (AnnexinV-FITC/PI assay), DNA fragmentation (cell cycle analysis), and cleavage of caspase-3 (Western blotting). In addition, c-myc is an oncogene essential for cell cycle progression in human tumor cells, and its suppression has been associated with decreased cell proliferation and arrest, predominantly in G0/G1 phase of the cell cycle.^85,86 The downregulation of c-myc that was detected in 7c-treated CEM cells opens the possibility that other analogues in the “series 7” may undergo c-myc dependent exit from the cell cycle and subsequent (apoptotic) death. Such may be the case with compound 7i, for example, considering the observation of G0/G1 phase arrest.

In Vivo Evaluation.

In vivo preclinical tumor growth inhibition has been regarded as an indispensable experiment to understand the expected activity of antitumor agents in humans and thus serves as important milestone in anticancer drug development. The most promising dual targeting derivative 7c, was further evaluated in vivo using a standard subcutaneous xenograft model produced using the CEM cell line. To investigate the capacity of compound 7c to inhibit murine tumor growth, SCID mice were implanted with CEM-derived tumor cells and the tumor allowed to grow to an approximate volume of 100 mm³. The animals were then assigned to three groups (n = 6 mice per treatment group) for treatment with control, Doxorubicin (20 mg/kg), or 7c (50 mg/kg). Treatments were given as described in the methods. As shown in Figure 11, administration of compound 7c significantly retarded tumor growth. This was reflected by reduction in tumor volume by ∼48% compared with the control group (Figure 11A) and a %TGI (tumor growth inhibition) of 24% on day 18. Body weights of the mice were not significantly affected by 7c or doxorubicin administration when compared to the control group, and there were no behavioral changes observed in any of the 7c treated mice. These results suggest that 7c significantly inhibits tumor growth with no signs of severe toxicity.

Figure 11. — (A) Growth curve of tumor volume vs time in CEM (T cell leukemia) xenografts treated with doxorubicin 20 mg/kg i.p.,7c 50 mg/kg i.p., untreated saline i.p. Error bars represent standard error of the mean (SEM) n = 6. p < 0.001. (B) Excised tumor image of the animals treated with doxorubicin 20 mg/kg i.p., 7c 50 mg/kg i.p., untreated saline i.p.

Many HDAC inhibitors and PPARγ agonists with antitumor capacity have been evaluated for in vivo efficacy, wherein both classes of drugs have showed effective tumor regression at relatively high doses from 50 mg/kg to 400 mg/kg, %TGI ranging from 9% (for low doses) to 40% (at higher doses), with animals showing no sign of severe toxicity. For example, the recently studied HDAC inhibitor belinostat has shown in vivo efficacy in pancreatic cancer at doses of 100 mg/kg in nude mice. Also, its combination with gemcitabine had synergistic effects.⁸⁷ Similarly, vorinostat was used at a concentration of 150 mg/kg in urothelial carcinoma.⁸⁸ Several other newer HDAC inhibitors have also been evaluated in vivo in various cancer models.^89–94 In the case of in vivo evaluation of PPARγ agonists in various cancer models, a similar trend is observed.^95–98 Hence, dual-targeting compound 7c with %TGI of 24% appears more potent than single-targeted agents. Considering its in vivo efficacy at higher doses, 7c analogues and other HDAC inhibitors or PPARγ agonists might be used as an adjuvant to existing chemotherapy to help reduce resistance/toxicity issues and possibly enhance antitumor effects in a synergistic manner. Hence, the in vivo combinatorial effects of compound 7c should be further evaluated.

CONCLUSIONS

The clinical effectiveness of recent single target anticancer drugs has been limited because of unexpected resistance and target nonspecificity. Among the attempts to tackle this concern, a strategy of multitargeting approach could be applied which would be able to hit multiple cancer hallmarks to achieve the desired pharmacological effectiveness with reduced detrimental effects. The combination treatment of HDAC inhibitors and PPARγ agonists increased the cytotoxic effects in a synergistic/additive manner against different cancer cell lines resulting in the arrest of proliferation and increased apoptosis. On the basis of this literature evidence, in an attempt to bring about a multitarget drug approach and simultaneously target HDAC/PPARγ, a series of 25 novel TZD-based naphthylidene derivatives were rationally designed and successfully synthesized. Complete biological evaluation of all compounds revealed their dual targeting ability by partial activation of PPARγ and selective inhibition of HDAC4. In our knowledge, this is the first ever attempt to develop agents that simultaneously target HDAC and PPARγ, two potential targets in cancer drug discovery. Out of 25 compounds synthesized several were found to inhibit HDAC4 effectively and Six compounds showed dual targeting activity with submicromolar potencies; the most potent dual targeting agent 7i had PPARγ EC₅₀ = 0.245 μM and HDAC4 IC₅₀ = 1.1 μM. Out of these six compounds, 7c and 7i were also found to exhibit antiproliferative effects against CEM cells with CC₅₀ values of 2.8 and 9.6 μM, respectively. Both of them also induced apoptosis and caused a significant DNA fragmentation in cell cycle analysis. Further, compound 7c was found to modulate the expression of c-Myc and cleave caspase-3 in Western blotting experiments. These in vitro antiproliferative effects were supported by in vivo tumor regression by compound 7c in CCRF-CEM tumor xenografts. Taken together, this study provides a theoretical basis for rational design of dual/multitargeting agents that could be developed further as anticancer therapeutics.