Heat Shock Protein 70 Inhibitors. 1. 2,5′-Thiodipyrimidine and 5-(Phenylthio)pyrimidine Acrylamides as Irreversible Binders to an Allosteric Site on Heat Shock Protein 70

Heat shock protein 70 (Hsp70) is an important emerging cancer target whose inhibition may affect multiple cancer-associated signaling pathways and, moreover, result in significant cancer cell apoptosis. Despite considerable interest from both academia and pharmaceutical companies in the discovery and development of druglike Hsp70 inhibitors, little success has been reported so far. Here we describe structure–activity relationship studies in the first rationally designed Hsp70 inhibitor class that binds to a novel allosteric pocket located in the N-terminal domain of the protein. These 2,5′-thiodipyrimidine and 5-(phenylthio)pyrimidine acrylamides take advantage of an active cysteine embedded in the allosteric pocket to act as covalent protein modifiers upon binding. The study identifies derivatives 17a and 20a, which selectively bind to Hsp70 in cancer cells. Addition of high nanomolar to low micromolar concentrations of these inhibitors to cancer cells leads to a reduction in the steady-state levels of Hsp70-sheltered oncoproteins, an effect associated with inhibition of cancer cell growth and apoptosis. In summary, the described scaffolds represent a viable starting point for the development of druglike Hsp70 inhibitors as novel anticancer therapeutics.


■ INTRODUCTION
The heat shock protein 70 (Hsp70) family members are powerful proteins with major roles in malignancy, such as inhibition of apoptosis, induction of resistance to chemotherapy, and regulation of the stability of oncoproteins. 1−3 Specifically, Hsp70 expression blocks apoptosis at several levels, and in this respect the chaperone inhibits key effectors of the apoptotic machinery, and also facilitates proteasome-mediated degradation of apoptosis-regulatory proteins. The contribution of Hsp70 isoforms to tumorigenesis is mainly through their role as cochaperones of heat shock protein 90 (Hsp90), a heat shock protein known to regulate the transforming activities of several kinases and transcription factors. In this process, Hsp70 initiates the association of the client protein with Hsp90 through a bridging protein called HSP-organizing protein (HOP). These biological functions propose Hsp70 as an important target whose inhibition or downregulation may result in significant apoptosis in a wide range of cancer cells and also in inhibition of signaling pathways involved in tumorigenesis and metastasis. Indeed, simultaneous silencing of Hsc70 or Hsp70 expression in human colon cancer cell lines induced proteasome-dependent degradation of Hsp90 onco-client proteins, cell-cycle arrest, and tumorspecific apoptosis. 4 Importantly, silencing of Hsp70 isoforms in nontumorigenic cell lines did not result in comparable growth arrest or induction of apoptosis, indicating a potential therapeutic window for Hsp70 targeted therapies. The Hsp70's are a family of highly homologous proteins composed of two functional domains: the N-terminal ATPase domain and the C-terminal client protein-binding domain. 5,6 The unique interplay between the two domains creates a ligandactivated, bidirectional molecular switch. For example, ATP binding to the ATPase domain induces a conformational change that is rapidly propagated to the C-terminal and that results in accelerated client protein dissociation. Conversely, client protein binding to the C-terminal domain of ATP-bound Hsp70 induces a conformational change that is propagated to the ATPase domain and that results in a stimulation of the ATP hydrolysis rate. The chaperoning activity of Hsp70 is further regulated by cochaperones (e.g., Hsp40s, BAG, and Hsp110) that catalyze the interconversion between the ATP-and ADP-bound states and thus regulate chaperone function. Such structural regulation suggests that Hsp70 may be vulnerable to most strategies that interfere with its flexibility.
Much effort has recently been dedicated toward the discovery of Hsp70 inhibitors, and unsurprisingly, molecules from a number of chemical classes have been reported to interact with Hsp70 through a variety of modes ( Figure 1). 7,8 A few, such as 15-deoxyspergualin (1) and pifithrin-μ (2-phenylethynesulfonamide) (2), are believed to target the C-terminal of Hsp70,9,10 whereas others, such as dihydropyrimidines (i.e., 3 (MAL3-101)), 11 are thought to block J-domain-stimulated ATPase activity of Hsp70. Compounds such as myricetin (4) 12 and 5 (MKT-077) 13 are proposed to interact with a pocket outside the nucleotide-binding domain, whereas apoptozole (6) may bind to the ATP-binding pocket of Hsp70. 14 The majority of these compounds were discovered in library screens that aimed to identify inhibitors of either the ATPase or the folding capacity of yeast or bacterial Hsp70 2,7,8 or in the case of 6 a cell-based screen of compounds capable of inducing apoptosis. 15 5 was discovered following optimization efforts 16 that had previously identified such rhodacyanine dyes as possessing anticancer activity. 17 In the only reported rational design approach to develop Hsp70 inhibitors, nucleotide mimetics such as the dibenzyl-8-aminoadenosine analogue 7 (VER-155008) were developed to bind into the N-terminal ATP pocket of Hsp70. 18 While these molecules are reported to elicit their effects through an Hsp70 mechanism, it is likely that they also act on multiple other unrelated and as yet unspecified mechanisms. Furthermore, these molecules have been hindered by a nontractable structure−activity relationship (SAR), with subtle changes resulting in drastic changes in activity. While these molecules have been of some value as tool molecules to offer insight into the consequences of pharmacological modulation of Hsp70, they have limited potential to become useful drugs.
At this point in time it is fair to say that Hsp70 has proven to be a very difficult target to drug. In contrast, Hsp90 has proven highly amenable with numerous small-molecule ATP-competitive inhibitors entering into the clinic. 19 In the case of Hsp90, potent small-molecule inhibitors such as geldanamycin and radicicol were known even before their precise mode of action was determined. When X-ray crystal structures showed that they bound to a clearly specified pocket (i.e., ATP pocket) and behaved as ATP-competitive inhibitors, structure-based drug design became possible. Unfortunately, no such molecules that could potentially guide and truly inspire the development of Hsp70 inhibitors exist for Hsp70.
The experiences of scientists at Vernalis offer some further insight into the difficulty of targeting Hsp70 and perhaps as to why no natural product ATP-competitive inhibitor is known. 18,20 In the only rational approach reported to date, they designed a series of adenosine analogues to act as direct ATP-competitive inhibitors. However, despite obtaining molecules that bound Hsp70 with high affinity (K d = 50 nM), their cellular potency was disappointing, and a number of reasons were given for this poor correlation. Hsp70 has a high affinity for ADP (K d = 0.11−0.5 μM) and coupled with high intracellular ATP concentrations makes the prospect of competitive inhibition a daunting task. Furthermore, the binding mode of ATP is such that important polar contacts are made with its βand γ-phosphate groups that lie buried within a polar cavity. Attempts to mimic these interactions have resulted in highly polar nondruglike molecules such as 7, which despite potent affinity (K d = 0.3 μM) possess weak cellular activity. Combined, these factors make the prospect of obtaining compounds with potent in vivo activity low and make a strong case against the development of reversible ATPcompetitive inhibitors of Hsp70 as a viable therapeutic strategy. 21 We had sought alternative strategies toward inhibiting Hsp70 which would have the potential for potent in vivo activity. Specifically, we had sought and subsequently identified another pocket, outside of the active site. 22 This allosteric site, located in the N-terminal domain, was not evident nor entirely predicted by the available crystal structures of Hsp70 and has been recently discovered by us through computational analyses. 22 We used the homology model to design ligands that could bind to this allosteric pocket. 22 Here we describe structure−activity investigations in this first reported allosteric pocket inhibitor class. These ligands are 2,5′-thiodipyrimidine and 5-(phenylthio)-pyrimidine scaffold compounds that we show here and in the accompanying paper 23 to be amenable to extensive medicinal chemistry and to act on cancer cells through an Hsp70-mediated mechanism.
■ LIGAND DESIGN AND COMPUTATIONAL

ANALYSIS OF LIGAND−HSP70 INTERACTIONS
There are several available crystal structures of Hsp70, but most capture a relatively closed nucleotide-binding domain. 24−27 In contrast, recent NMR techniques and molecular dynamics studies suggest a model in which subdomains of the N-terminus are bridged and in a close proximity only in the ATP-binding conformation, with residues of these subdomains rearranging and the cleft opening upon ADP binding. 28,29 To overcome these limitations of the currently available crystal structures and to investigate pockets other than the ATP-binding site, we recently developed a theoretical model of human Hsp70 (hHsp70). 22 This nucleotide-free structure of hHsp70 both captured the Nterminal binding cleft in a conformation that is more open than that captured by X-ray and unveiled a pocket that contains a potentially reactive cysteine residue (Cys267 in hHsp70) embedded inside the cavity (Figure 2a). 22 The newly identified allosteric pocket (depicted by the green surface in Figure 2a  (c) The geometry of the N-terminal allosteric pocket of hHsp70 as predicted by SiteMap (shown in yellow) and residues lining the pocket and their relative location (depicted as colored circles) are presented. Ligands based on the 2,5′-thiopyrimidine and 5-(phenylthio)pyrimidine chemical scaffolds were designed to fit into the allosteric pocket. They adopt the conformation required for a proper fit and position functionalities toward the shown pocket residues. An acrylamide positioned toward Cys267 was also incorporated into these scaffolds. This cavity is larger and potentially more druglike than the nucleotide-binding pocket (depicted by the red surface in Figure  2b), because it contains a balanced number of hydrophilic and hydrophobic residues (Figure 2c). At the lower part of the allosteric site lies mainly a hydrophilic cavity containing Lys271 and Glu268 and further apart lined by Thr13, Thr14, Tyr15, Lys56, Asp234, Asn235, Arg264, Thr265, and Arg269 (numbering as in hHsp70) (site A, Figure 2c). Hydrophobic amino acids such as Leu237 and Val238 also line site A. This subpocket also contains the potentially reactive cysteine residue, Cys267, that could covalently link to a ligand containing the appropriate Cysreactive functionality, such as an acrylamide. 30 Adjacent to site A, and placed in the middle, is a larger cavity comprised of both nonpolar and polar amino acid residues, such as Tyr41, Val59, Pro63, Thr66, Asp69, Phe68, Arg72, Glu231, Val260, and Arg261 (site B, Figure 2c). Placed at the upper part of the binding site, and also potentially providing interactions to a smallmolecule ligand, are Lys88, His89, Trp90, Pro91, and Phe92 (site C, Figure 2c).
We analyzed the geometry and the environment of the computationally identified allosteric pocket to provide a starting point for the rational design of ligands ( Figure 2c). We concluded that ligands built around the 2,5′-thiodipyrimidine and 5-(phenylthio)pyrimidine scaffolds, both little explored chemical spaces, would adapt the necessary conformation and provide the required attachment sites for ligand functionalization (Figure 2c). Each designed ligand used this pharmacophore template to attach X 3−7 functionalities pointed toward several amino acids lining the Hsp70 pocket (Figure 2c). Because our homology model may not entirely mimic the native protein structure, we included an additional binding hook, i.e., an acrylamide functionality, to probe possible covalent bond formation between the inhibitor and Cys267 upon protein binding (Figure 2c). Due to the location of Cys267 deep inside the cavity, such bond formation would be possible only after the ligand was inserted into the pocket and has achieved a proper fit. By gaining affinity through a covalent linkage in addition to enthalpy, we hoped to increase the ligand's apparent affinity for the protein in the event the fit would be less than optimal. We reasoned that if the initial ligand would be of sufficiently good fit, additional enthalpy could be gained by properly modifying the appended functionalities, such as we proceed to do here and in the adjoining paper. 23

■ CHEMISTRY
The synthesis of all designed compounds evaluated in this study is shown in Schemes 1−3 and described below. Reaction of 2amino-4,6-dimethoxypyrimidine (8a) with p-methoxybenzyl chloride ((PMB)Cl) resulted in PMB-protected pyrimidine 9a in 95% yield (Scheme 1). This was iodinated with Niodosuccinimide (NIS) to give 10a in 98%, which was further coupled to 4,6-diamino-2-mercaptopyrimidine using CuI/neocuproine to give 2,5′-thiodipyrimidine 11a in 65% yield. Acetylation of the amino groups was accomplished with Ac 2 O/ DMAP at 110°C for 2 h to give 12a in 91% yield. Selective removal of the PMB groups occurred by heating 12a in a 1:1 mixture of TFA/CHCl 3 at 62°C for 24 h to give 13a in 95%. Fluorodediazoniation was accomplished with NaNO 2 /HF/ pyridine to give 14a in 54% yield, which was then reacted with a variety of amines to yield 15a−c. Deacetylation of these intermediates followed by reaction with acryloyl chloride resulted in target compounds 17a−c. Derivatives 20a−c were prepared following a similar route from 2-amino-4,6-diethoxypyrimidine (8b), which was prepared by refluxing a mixture of 2-amino-4,6-dichloropyrimidine and NaH in ethanol in 89% yield (Scheme 1).
The chemistry used to prepare 27a−d is similar and shown in Scheme 1. Derivative 10a was coupled with 4-amino-2mercaptopyrimidine to give 21 in 92% yield. Acetylation followed by PMB removal resulted in 23. Reaction with NaNO 2 /HF/pyridine gave fluoro derivative 24, which was reacted with a variety of amines to give 25a−d. Deacetylation followed by reaction with acryloyl chloride resulted in target compounds 27a−d. Reaction of 27a with m-CPBA at −78°C resulted in N-oxide 28. Reaction of 24 with NaOMe/MeOH followed by deacetylation resulted in 29, which was reacted with acryloyl chloride to give 30 (Scheme 2). Reaction of 11a with acryloyl chloride followed by treatment with TFA resulted in 31 (Scheme 2).
Thioethers shown in Scheme 3 were prepared from chloropyrimidine 32 or 38. Reaction of 32 with N-methylpiper-  azine or morpholine resulted in 33a and 33b, respectively. Iodination of these derivatives, followed by coupling with 3aminothiophenol resulted in 35a and 35b, respectively. These compounds were then reacted with a variety of unsaturated acid chlorides to give target compounds 36a,b and 37. Target compounds 42a−c and 43 were prepared similarly starting from chloropyrimidine 38 (Scheme 3).

INHIBITOR SERIES
Recent studies suggest that, unlike normal cells, cancer cells express modified heat shock protein species characterized by both enhanced cochaperone recruitment and distinct posttranslational modifications. 31−33 Evidence also indicates that certain small molecules show preferential binding to these To confirm an Hsp70-mediated mechanism, it is expected that compounds will be active at similar concentrations in this battery of assays. Table 1 compd tumor-modified heat shock proteins. 32 Our goal being to develop Hsp70 inhibitors for cancer treatment, we accordingly employed here a testing strategy that used phenotypic assays to read fingerprints of Hsp70 inhibition in tumor cells rather than a classical recombinant protein-based approach ( Figure 3). To design a tumor−Hsp70 tailored testing module, we took advantage of known biological activities mediated by Hsp70 in cancer. As mentioned, Hsp70 is both an antiapoptotic molecule 4 and a transforming protein that acts together with Hsp90 to regulate the altered activity of several cancer kinases. 1,2,34 Thus, our testing strategy incorporated assays that measured induction of apoptosis (i.e., the ability to activate caspase-3,7, Tables 1 and 2 and induce PARP cleavage, Table 3) and those that read a phenotypic outcome similar to that of Hsp90 inhibitors (i.e., degradation of Hsp90/Hsp70-sheltered oncoproteins such as HER2 and Raf-1 in the proper genetic background, Table 3) (see tests 1 and 2 in Figure 3). Because a compound that interferes with nucleotide binding to the ATP-binding pocket of Hsp90, either competitively or allosterically, could result in a phenotype closely resembling Hsp70 inhibition, we also included an assay to test for possible direct binding to Hsp90 (Table 3).
HER2 is a key transforming protein in the HER2-overexpressing breast cancer cells SKBr3, and its degradation or inhibition is sufficient to inhibit the growth of these cells. Thus, in addition to testing the effect of these derivatives on HER2 expression, we also measured their activity on cell growth (Table   3). 35,36 In addition, the compounds were further tested for their ability to inhibit the growth of cancer cells of distinct genetic origin, including the P-gp/MDR-1-expressing Kasumi-1 acute myeloid leukemia cells (Table 1) (see test 3 in Figure 3). Table 2 a Inhibition of growth measured in Kasumi-1 acute myeloid leukemia cells. Values are the mean ± SEM. b Caspase-3,7 activation measured in MOLM13 acute myeloid leukemia cells. Values are the mean ± SEM. For select derivatives we probed their ability to bind Hsp70 from tumor extracts ( Figure 4a) and from live cancer cells (Figure 4b,c) and investigated their ability to alter the Hsp70− HOP complex in cancer cells (Figure 4d; see test 4 in Figure  3). 5,6,32 For a specific Hsp70-mediated biological effect it is expected that compounds should act with a similar potency in the abovedescribed battery of assays (for example, the IC 50 measured in the client degradation assay should be near the IC 50 measured in Hsp70−HOP complex alteration and so on). 2,35,36 Inclusion in the testing module of three different Hsp70-addicted cell lines, including one P-gp/MDR-1 expressing, increased our likelihood to eliminate early on poorly permeable compounds and those marred by potential for P-gp/MDR-1-induced resistance.

HSP70 INHIBITOR SERIES
In addition to ligand design, we used the homology model to investigate structure−activity relationships in the designed Hsp70 inhibitor series ( Figure 5). To study potential ligand− protein interactions, we docked each derivative into the allosteric site. This strategy, combined with the phenotypic, target-derived biological investigation (Figure 3), as described above, was used , and D-biotin, the unbound agent was washed off, and the resulting beads carrying 44b, 45b, or D-biotin were probed with SKBr3 cell extracts (500 μg). Hsp70 isolated on the beads was probed by Western blot (WB). A representative blot is presented (top). Blots were quantified by densitometry and values, in relative luminescence units, graphed against the concentration of added biotinylated Hsp70 inhibitor (bottom). Results from three independent experiments were graphed to determine the relative binding affinity (K d ) of 44b and 45b using equations as implemented in the GraphPad Prism software. Key: points, mean; bars, SD. (b) Cells were treated with the indicated concentrations of 44b for 6 h prior to lysing and precipitation of protein complexes on streptavidin beads. Beads were washed with high-salt (1 M NaCl) buffer before elution of proteins on a denaturing gel and silver staining. BB70 is an antibody specific for Hsp70. This antibody also recognizes Grp78 and Grp75, the endoplasmic reticulum and the mitochondrial Hsp70 paralogues, respectively. (c) Protein complexes were isolated as indicated in (b) in cells pretreated with 17a. CP = chemical precipitation. (d) Analysis of the Hsp70−HOP complex. SKBr3 cells were treated for 24 h with vehicle or indicated concentrations of 20a. Upon cell lysing, Hsp70 complexes were isolated with an anti-Hsp70 antibody (IP BB70) and analyzed by WB. Specificity of binding was tested with a control IgG. Gels were quantified by densitometry, values normalized to the control (vehicle only treated cells), and data graphed against the concentration of 20a. Error bars represent the SEM (n = 2). to understand differences in tumor Hsp70 inhibitory activity among the designed derivatives.
Site C. Attached to ring A is substituent X 7 pointing toward the exit of the binding site (Figure 2c). At this position we could accommodate a variety of substituents such as piperazine, morpholine, piperidine, pyrrolidine, methoxy, and amino (Table  1). Methylpiperazine, however, was preferred over all others (17a versus 17b, 17c, and 31; 20a versus 20b and 20c; 27a versus 27b, 27c, 27d, and 30; 36a versus 37). At physiological pH, methylpiperazine is likely to be protonated, and this H is predicted by docking to form a hydrogen bond interaction with the backbone carbonyl of His89 ( Figure 5). Indeed, an approximately 10-fold drop in activity was observed when the N-Me of methylpiperazine was substituted with O (as in morpholine) or C (as in piperidine). Additionally, when this amine was oxidized to the corresponding N-oxide, as in derivative 28, activity was almost abolished, potentially due to the unfavorable interaction of the N-oxide oxygen with the backbone carbonyl of His89. The pyrrolidine-containing derivative 27d had a poor aqueous solubility, which likely accounted for the erratic cellular activity we observed for this compound.
Site B. Substituents X 5 and X 6 of ring A are placed in the middle cavity of the binding site comprised of both nonpolar and polar amino acid residues, as described above (Figure 2c). Substituents at these positions, such as methoxy, ethoxy, and methyl, were well tolerated (compare 17a (methoxy), 20a (ethoxy), and 42a (methyl)). Modeling predicts for such substituents a potential for hydrophobic (alkyl portion of these substituents with Val59) and electrostatic (oxygen of methoxy and ethoxy with Arg261) interactions ( Figure 5), and all derivatives containing these substituents had favorable biological activity. Modeling also indicated the potential for steric clash for X 5 and X 6 substituents of larger size, such as in 45a, and indeed, we observed a substantial loss of activity for this derivative (Table  1).
Site A. At the bottom of the allosteric pocket lies Cys267, which is predicted to form a covalent bond with the acrylamide positioned at X 4 on ring B ( Figure 5). The contribution of the acrylamide moiety toward covalent binding with the protein can be seen by comparing compounds in which it is attached to either a pyrimidine or phenyl ring. Since the two nitrogen atoms of the pyrimidine ring render the ring more electron deficient, acrylamide functions attached to it would be expected to be more active Michael acceptors than in the corresponding phenyl compounds. Indeed, a trend for increased activity was seen for the pyrimidine-based compounds when compared to the similar phenyl derivatives (Table 1, 27a and 27b versus 36a and 37, respectively).
In addition to covalent Cys modification, the acrylamide substituent at position X 4 is poised to form several interactions with the adjacent protein residues ( Figure 5). Specifically, the alkene group is positioned to establish hydrophobic interactions with Leu237 and Val238. The carbonyl group is poised to form electrostatic interactions with the guanidine group of Arg264, ε-NH 2 of Lys271, and backbone −NH of Glu268 and could potentially also form hydrogen bonds with the surrounding residues.
To further understand the contribution of the acrylamide to binding, we prepared several methyl-substituted acrylamide derivatives ( Table 2). Each of these derivatives was found to be less active than the unsubstituted acrylamide derivatives (36a versus 36b; 42a versus 42b and 42c). This decrease in reactivity can be explained by both steric and electronic effects. The methyl group could act to sterically hinder nucleophilic attack by the reactive cysteine residue (Cys267). Furthermore, the methyl group is a mild electron-donating group and would decrease the electrophilicity of the Michael acceptor.
Ring B occupies the lower part of the binding site which also contains Arg264. Thus, the aromatic rings that were designed to compose ring B, such as phenyl and pyrimidine, are predicted to be stabilized by cation−π interactions with the guanidine group of this arginine residue ( Figure 5). Ring B also orients substituents toward several important pocket residues. Specifically, at the lower part of the pocket are Asp234 and Glu268, which have the potential to interact with substituents on ring B, such as those located at position X 3 ( Figure 5). Accordingly, derivatives for which X 3 was NH 2 (i.e., 17a) were more potent than similar derivatives having a hydrogen at this position (i.e., 27a) potentially because NH 2 could form hydrogen bonds with the carboxylate groups of Asp234 and Glu268.

■ EVALUATION OF SELECTIVITY AND
TARGET-MEDIATED CELLULAR ACTIVITY From these studies, derivatives 17a and 20a emerged as most active (Tables 1 and 3). Next, we attached 17a to biotin with two aims in mind, first, to demonstrate effective and selective isolation of Hsp70 from cancer cells by 17a and, second, to further validate that the acrylamide was not the sole contributor to ligand−protein binding. Specifically, we have created two derivatives of 17a by attaching to it linkers that allow for biotin modification of 17a (Figure 4a). In derivative 44a, the linker was attached from the piperazine ring and thus predicted to point outside the allosteric pocket. Indeed, 44a retained biological activity similar to that of 17a (Tables 1 and 3). In derivative 45a, the linker was attached on ring A through substituent X 5 , thus at a position that would create steric clashes between the substituent and Hsp70 (Figure 4a). Indeed, 45a was of much reduced activity when compared to 17a (Tables 1 and 3). We next attached 44a and 45a to biotin and then immobilized, dose-dependently, the resulting 44b and 45b biotin-labeled ligands onto streptavidincontaining beads. We then used these beads to isolate Hsp70 from cancer cell extracts.
As expected from a mode of binding in which enthalpy substantially contributes to binding, efficient isolation of Hsp70 from a cancer cell extract was observed for the beads containing derivative 44b but not 45b (Figure 4a). If binding were solely driven by covalent modification through the acrylamide functionality, both 44b and 45b would interact equally well with Hsp70 and, thus, isolate similar amounts of Hsp70 from the cell extract. In conclusion, a proper fit into the protein pocket in addition to covalent modification was important for the ability of these ligands to bind to and inhibit Hsp70.
To demonstrate the selectivity of interaction, we incubated cancer cells with 44b and then proceeded to isolate the captured proteins on streptavidin beads. Upon washing the affinitypurified complexes and running them on a denaturing gel, the selectivity of 44b toward Hsp70 was demonstrated by the presence of a single band upon silver staining (Figure 4b). This band as demonstrated by its size of 70 kDa, its ability to run at a position identical to that of the protein isolated by an anti-Hsp70 antibody (Figure 4b, BB70), and its recognition by an Hsp70specific antibody ( Figure 4a) and mass spectrum analysis 22 corresponds to Hsp70. Furthermore, preincubation of cells with soluble 17a prior to affinity purification led to a dose-dependent reduction of immobilized Hsp70, demonstrating the specificity of the interaction (Figure 4c). Altogether, these findings confirm that the designed ligands act in cells by specifically binding to Hsp70. When cancer cells were incubated with select derivatives (i.e., 20a), we observed a dose-dependent alteration in the formation of Hsp70−HOP complexes in cancer cells ( Figure 4d). As mentioned above, HOP is a cochaperone that bridges Hsp70 and Hsp90 to form a megachaperone complex (see test 4 in Figure  3). This chaperone machinery regulates the stability of several onco-client proteins, such as HER2 and Raf-1, whose degradation, as caused by chaperone inhibition, was tested here (Table 3). Of importance, alteration in the Hsp70−HOP complex formation occurred at the same low concentrations (IC 50 = 1.73 μM, Figure 4d) where we also observed degradation of HER2 and Raf-1 by this inhibitor (1 and 2.5 μM, respectively, Table 3), further supporting the Hsp70-mediated mechanism of action of these ligands.
We noted no effect on Hsp90 for the ligands reported here at concentrations as high as 500 μM (Table 3). Specifically, unlike the direct Hsp90 inhibitor PU24FCl, 38 a compound with cellular activity comparable to that of the most active Hsp70 inhibitors described here, such as 17a and 20a (Table 3, HER2, Raf-1), the Hsp70 inhibitors failed to compete with a fluorescently labeled geldanamycin derivative, GM-Cy3B 39 for Hsp90 binding (Table  3). Geldanamycin is an Hsp90 inhibitor that binds to the Hsp90 regulatory pocket 37 located in the N-terminal domain of Hsp90. The fluorescence polarization based Hsp90 assay that incorporates GM-Cy3B is designed in such a way that it probes not only for direct binders to the ATP pocket but also for those compounds that may allosterically interfere with the conformation of Hsp90 to block compound access to the ATP pocket.
We also tested myricetin (4; Figure 1) in these assays (Table  3). Using NMR techniques, 12 this compound was proposed to interact with the bacterial Hsp70 homologue, DnaK, at a site potentially close to that occupied by our designed Hsp70 inhibitors. 4 was also recently reported to inhibit the DnaK− DnaJ (bacterial Hsp70−Hsp40) complex formation (IC 50 = 14.5 μM). 12 We could however not measure Hsp70-mediated biological effects for 4 in the SKBr3 cancer cells at concentrations as high as 100 μM, possibly due to the poor stability of 4 in the cells. Indeed, LC/MS−MS analyses of cellular extracts demonstrated rapid myricetin degradation with the agent virtually undetectable after 10 min of incubation (not shown). Interestingly, when tested for its potential to bind Hsp90, we found 4 to alter geldanamycin's binding to Hsp90 (Table 3). Polyphenols such as 4 are recognized for their high propensity to bind nonspecifically to proteins. As such, caution must be taken when interpreting biological and biochemical results derived through the use of such compounds.
Next, we tested select lead compounds in vitro for potential to interfere with other proteins. At the physiologically relevant concentration of 10 μM, derivative 17a was inert when tested against the scanMAX 402 kinase panel ( Figure 6). This panel contains a set of kinases covering the AGC, CAMK, CMGC, CK1, STE, TK, TKL, lipid, and atypical kinase families, plus important mutant forms. Developed by Ambit Biosciences, it employs proprietary active-site-dependent competition binding assays to determine how compounds bind to kinases. It is based on a competition binding assay that quantitatively measures the ability of a compound to compete with an immobilized, activesite-directed ligand and can be used in detection of multiple inhibitor types (e.g., types I and II and non-ATP-competitive). 40,41 ■ CONCLUSIONS In summary, we describe here SAR studies in the first rationally designed scaffolds with binding potential to a novel allosteric pocket in human Hsp70. This site is located in the N-terminal domain of the chaperone and was recently identified by our homology modeling studies. 22 It is not revealed by reported crystal structures of Hsp70, as these capture the protein in a closed conformation in which the reactive Cys267 is unavailable for ligand binding and the pocket is narrow. 24−27 The designed ligands are of a yet unexplored chemical space based on the 2,5′thiodipyrimidine and 5-(phenylthio)pyrimidine scaffolds, and thus, we are also first to report here a chemical strategy that allows for the assembly of such compounds.
The weight of the evidence in this paper and in our previous report 22 indicates that these compounds are acting on Hsp70 through binding to the allosteric pocket. Only if reasonably correct could the homology model enable the rational design of a ligand that, when incubated with the thousands of proteins expressed in a cancer cell, substantially affinity purifies one, Hsp70. Seconded by a biological investigation of these ligands based on specific modulation of the target, Hsp70, in the context of a cancer cell, our data clearly define the mode of action of these ligands, in the cancer cell, through inhibition of Hsp70. From these studies, we identify derivatives 17a and 20a as being the most active of the series. Addition of high nanomolar to low micromolar concentrations of these agents to several cancer cells led to a reduction in the steady-state levels of Hsp70−HOP− Hsp90 complex chaperoned oncoproteins, an effect associated with inhibition of cell growth and apoptosis.
Because Hsp70 contains an active cysteine embedded in the allosteric pocket, the derivatives presented herein contain an acrylamide functionality that may create a covalent bond with such a residue upon Hsp70 protein binding. We have used several techniques to demonstrate the potential formation of a covalent bond between the inhibitor and the protein. 22 First, when the biotinylated analogue of 17a, 44b, was incubated with cancer cells, we noted a time-dependent progressive increase in the amount of immobilized Hsp70. This profile is indicative of time-dependent covalent modification of the protein and is specific for compounds such as 17a, where irreversible binding plays a role. Second, mass spectrum analysis of the trypsin digest of the 44b−Hsp70 complex identified a major m/z peak at 1867.915. 22 This corresponds to 44b bound to LRTAC 267 ERAK and confirms that the site of interaction of 17a with Hsp70 is within site 1, where Cys267 is located and, furthermore, that 17a forms an irreversible bond with the protein upon binding. Third, when we probed binding of 44b to both the WT Hsp70 protein and the C267S mutant, we noted that high-salt, high-detergent conditions eluted preferentially the Hsp70-C267S mutant protein over the WT form from preformed Hsp70−44b complexes.
There is precedent for the use of an acrylamide "warhead" in the development of several irreversible kinase inhibitors currently in clinical trials for cancer. 42−46 There is, of course, a concern that such an entity could indiscriminately react with non-target-related proteins, resulting in unwanted biological effects. However, in spite of the presence of an acrylamide, derivatives described here are not excessively reactive and, in addition, have an appropriate fit in the active site of the target, anticipating a favorable enthalpic effect. It is also important to note that, for proteins with long half-lives, such as Hsp70, 47 irreversible inhibition is mechanistically advantageous as it confers complete target inhibition until resynthesis of the target protein 48 and thus allows for less frequent dosing, which may also tip the balance toward a better therapeutic index for such compounds.
In addition to providing both a novel pharmacophore and medicinal chemistry for its assembly, in this paper we describe a testing battery for assessing Hsp70-mediated mechanisms in cancer cells and for evaluating specific ligand action in cells through Hsp70 inhibition. Altogether, these findings provide a novel blueprint for a cancer-oriented development of Hsp70directed ligands.
To conclude, the series of novel chemical entities reported herein interact with a yet unexplored pocket in Hsp70. These compounds of tractable SAR favorably permeate cancer cells and exhibit their biological activity through inhibition of the tumor Hsp70 species, validating the scaffold as an important starting point for the development of Hsp70 inhibitors with potential therapeutic applications. The accompanying paper in this issue describes the synthesis and structure−activity evaluation of inhibitors of this series that target the same allosteric pocket of Hsp70 described herein but act through a reversible mechanism of action. 23 ■ EXPERIMENTAL SECTION Chemistry. All reagents were purchased from either Aldrich or Acros Organics and used without purification. All reactions were performed under argon protection. NMR spectra were recorded on a Bruker AV-III-500 MHz NMR spectrometer. Chemical shifts are reported in δ values in parts per million downfield from TMS as the internal standard. 1 H data are reported as follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, br = broad, m = multiplet), coupling constant (Hz), integration. 13 C chemical shifts are reported in δ values in parts per million downfield from TMS as the internal standard. Highresolution mass spectra were recorded on a Waters LCT Premier system. Low-resolution mass spectra were obtained on a Waters Acquity Ultra Performance LC instrument with electrospray ionization and an SQ detector. Analytical HPLC was performed on a Waters Autopurification system with PDA, MicroMass ZQ, and ELSD detectors. The purity of the title compounds used in pharmacology testing was determined by HPLC−MS using the following method: 10− 12 min gradient on a Waters2525 binary gradient pump of increasing concentrations of acetonitrile in water (5% → 95%) containing 0.1% formic acid with a flow rate of 1.2 mL/min and UV detection at λ = 220 and 254 nm on an XBridge C18 150 mm × 4.6 mm, 5 μm column. Title compounds used in pharmacology testing were >95% pure. Analytical thin-layer chromatography was performed on 250 μM silica gel F 254 plates. Preparative thin-layer chromatography was performed on 1000 μM silica gel F 254 plates. Flash column chromatography was performed employing 230−400 mesh silica gel. Solvents were HPLC grade. Myricetin was purchased from Indofine Chemical Co. (Hillsborough, Figure 6. Derivative 17a (at 10 μM) was tested in the scanMAX screen (Ambit) against 402 kinases. The TREEspot interaction map for 17a is presented. Only c-Met (red dot on the kinase tree) appears as a potential low-affinity kinase hit of 17a. KINOMEscan's selectivity score (S) is a quantitative measure of compound selectivity. It is calculated by dividing the number of kinases that bind to the compound by the total number of distinct kinases tested, excluding mutant variants. S(35) = (number of nonmutant kinases with %Ctrl < 35)/(number of nonmutant kinases tested). NJ). The synthesis of compounds 44a,b and 45a,b is described in detail in the Supporting Information.
Competition Assay. Cancer cells were pretreated for 2 h with increasing concentrations of 17a and then lysed in a buffer containing 20 mM Tris, pH 7.4, 25 mM NaCl, and 0.1% NP-40. Meanwhile, to prepare the 44b−streptavidin bead conjugates, 44b (50 μM) was added to highcapacity streptavidin agarose beads (Thermo Scientific) (30 μL per experimental sample), incubated for 1 h at 4°C, and then washed with lysis buffer. Protein extracts (500 μg of total protein) were then incubated overnight with the 44b−streptavidin bead conjugate. The complexes were washed in high-salt buffer, applied to SDS−PAGE, and stained with the SilverQuest staining kit (see Figure 4c).
Hsp70−HOP Complex Analysis. SKBr3 cells were treated with the indicated concentrations of the inhibitor for 24 h. Samples were collected and lysed in 20 mM Tris, pH 7.4, 25 mM NaCl, 0.1% NP-40 buffer with protease inhibitors added. Aliquots of 500 μg of total protein adjusted to 100 μL with the lysis buffer were prepared. Samples were incubated with 5 μL of BB70 antibody (Stressmarq) or normal IgG (as a negative control) and 20 μL of protein G agarose beads (Upstate) at 4°C overnight. Samples were washed five times with the lysis buffer and applied to SDS−PAGE followed by a standard Western blotting procedure to detect levels of HOP protein in the Hsp70 complexes upon treatment.
Growth Inhibition Assay. We evaluated the antiproliferative effects of inhibitors using the dye Alamar Blue. This reagent offers a rapid objective measure of cell viability in cell culture, and it uses the indicator dye resazurin to measure the metabolic capacity of cells, an indicator of cell viability. Briefly, cells were plated on Costar 96-well plates. For attached cells (such as SKBr3), 8000 cells/well were used. For suspension cells (such as Kasumi-1), 20000 cells/well were plated. Cells were allowed to incubate for 24 h at 37°C before drug treatment. Drugs were added in triplicate at the indicated concentrations, and the plate was incubated for 72 h. Alamar Blue (50 μM) was added and the plate read 6 h later using the Analyst GT (fluorescence intensity mode, excitation 530 nm, emission 580 nm, with a 560 nm dichroic mirror). Results were analyzed using the Softmax Pro software. The percentage cell growth inhibition was calculated by comparing fluorescence readings obtained from treated versus control cells, accounting for the initial cell population (time zero). IC 50 was calculated as the drug concentration that inhibits cell growth by 50%.
Caspase-3,7 Activation. 50 MOLM-13 cells (30000 cells/well) were plated in black 96-well plates (Corning no. 3603) in 40 μL of RPMI medium and left in an incubator (37°C, 5% CO 2 ) for up to 24 h. Cells were treated for 16 h with compounds or DMSO (control) at the desired concentrations in 50 μL of medium. Drugs were added in triplicate wells. Following exposure of cells to Hsp70 inhibitors, 50 μL of buffer containing 10 mM HEPES (pH 7.5), 2 mM EDTA, 0.1% CHAPS, and the caspase substrate Z-DEVD-R110 at 25 μM was added to each well. Plates were incubated until the signal stabilized, and then the fluorescence signal of each well was measured in an Analyst GT microplate reader. The percentage increase in apoptotic cells was calculated by comparison of the fluorescence reading obtained from treated versus control cells.
Kinase Screen. For most assays, kinase-tagged T7 phage strains were grown in parallel in 24-well blocks in an Escherichia coli host derived from the BL21 strain. E. coli were grown to log phase and infected with T7 phage from a frozen stock (multiplicity of infection 0.4) and incubated with shaking at 32°C until lysis (90−150 min). The lysates were centrifuged (6000g) and filtered (0.2 μm) to remove cell debris. The remaining kinases were produced in HEK-293 cells and subsequently tagged with DNA for qPCR detection. Streptavidincoated magnetic beads were treated with biotinylated small-molecule ligands for 30 min at room temperature to generate affinity resins for kinase assays. The liganded beads were blocked with excess biotin and washed with blocking buffer (SeaBlock (Pierce), 1% BSA, 0.05% Tween 20, 1 mM DTT) to remove unbound ligand and to reduce nonspecific phage binding. Binding reactions were assembled by combining kinases, liganded affinity beads, and test compounds in 1× binding buffer (20% SeaBlock, 0.17× PBS, 0.05% Tween 20, 6 mM DTT). Test compounds were prepared as 40× stocks in 100% DMSO and directly diluted into the assay. All reactions were performed in polypropylene 384-well plates in a final volume of 0.04 mL. The assay plates were incubated at room temperature with shaking for 1 h, and the affinity beads were washed with wash buffer (1× PBS, 0.05% Tween 20). The beads were then resuspended in elution buffer (1× PBS, 0.05% Tween 20, 0.5 μM nonbiotinylated affinity ligand) and incubated at room temperature with shaking for 30 min. The kinase concentration in the eluates was measured by qPCR. KINOMEscan's selectivity score (S) is a quantitative measure of compound selectivity. It is calculated by dividing the number of kinases that bind to the compound by the total number of distinct kinases tested, excluding mutant variants. TREEspot is a proprietary data visualization software tool developed by KINOMEscan. Kinases found to bind are marked with red circles, where larger circles indicate higher affinity binding. The kinase dendrogram was adapted and is reproduced with permission from Science and Cell Signaling Technology, Inc.
Computational Studies. All computations were carried out on an HP workstation xw8200 with the Ubuntu 8.10 operating system using Maestro v8.5 (Schrodinger LLC, New York). Grids were prepared using the Receptor Grid Generation tool in Glidev4.0. Docking calculations were run in the standard precision (SP) mode of Glide v4.0. The maxkeep variable, which sets the maximum number of poses generated during the initial phase of the docking calculation, was set to 5000, and the keep best variable, which sets the number of poses per ligand that enter the energy minimization, was set to 1000. The energy minimization protocol includes a dielectric constant of 4.0 and 1000 steps of conjugate gradient. Upon completion of each docking calculation, at most 100 poses per ligand were allowed to generate. The best docked conformation was chosen considering the orientation and Glidescore (G-score). 22 ■ ASSOCIATED CONTENT

* S Supporting Information
Description of the synthesis of compounds 44a,b and 45a,b. This material is available free of charge via the Internet at http://pubs. acs.org.

Accession Codes
The PDB ID codes of crystal structures used as a starting point for building the homology model are 1S3X, 2KHO, and 2P32.