4-Pyridylanilinothiazoles that selectively target von Hippel-Lindau deficient Renal Cell Carcinoma cells by inducing autophagic cell death
Renal cell carcinomas (RCC) are refractory to standard therapy with advanced RCC having a poor prognosis; consequently treatment of advanced RCC represents an unmet clinical need. The von Hippel-Lindau (VHL) tumor suppressor gene is mutated or inactivated in a majority of RCCs. We recently identified a 4-pyridyl-2- anilinothiazole (PAT) with selective cytotoxicity against VHL-deficient renal cells mediated by induction of autophagy and increased acidification of autolysosomes. We report exploration of structure-activity relationships (SAR) around this PAT lead. Analogues with substituents on each of the three rings, and various linkers between rings, were synthesized and tested in vitro using paired RCC4 cell lines. A contour map describing the relative spatial contributions of different chemical features to potency illustrate a region, adjacent to the pyridyl ring, with potential for further development. Examples probing this domain validated this approach and may provide the opportunity to develop this novel chemotype as a targeted approach to the treatment of RCC.
Introduction<!>Synthesis<!>Alignment Generation<!>3D-QSAR Analysis<!>Biological Assays<!>Results and Discussion<!>3D-QSAR model for cell cytotoxicity for the PAT series<!>Conclusions<!>Chemistry<!>Example of Synthetic Methods<!>Method A. Preparation of Pyridyl 2-Bromoethanones<!>Method B. Preparation of Thioureas<!>Method C. Alternative Preparation of Thioureas<!>Method D. Preparation of Thiazoles<!>Method E. Preparation of Pyridyl Amides<!>Method F. Preparation of Pyridyl Ketones<!>GI50 assays<!>Clonogenic assays<!>
<p>Renal cell carcinomas (RCC) represent a small, but significant fraction of adult malignancies1 and are refractory to standard chemotherapy and radiotherapy. Up to 45% of patients present with locally advanced or metastatic disease2 and these patients have an extremely poor prognosis.3 The current standard of care, immunotherapy using interferon or interleukin-2, has modest success with responses in a small fraction of patients with metastatic RCC.4 Although the recent introduction of anti-angiogenic therapies such as sunitinib (Sutent) and sorafenib (Nexavar) have provided modest responses it remains unclear which patients will have durable responses. This, combined with the observation of stable or increasing patient mortality, 5 defines the treatment of advanced RCC as an unmet clinical need.</p><p>The von Hippel-Lindau (VHL) tumour suppressor gene is inactivated in ca. 75% of RCCs.6,7 This gene encodes for an E3 ubiquitin ligase that specifically regulates the protein stability of a family of transcription factors called Hypoxia Inducible Factors (HIF).8 Loss of VHL results in constitutive expression of HIF leading to increased transcription of genes involved in metabolism, angiogenesis, invasion and metastasis, and proliferation leading to an aggressive phenotype.9–13 In addition to its role in HIF regulation, pVHL has been implicated in a variety of HIF-independent processes.14–17</p><p>We recently developed a synthetic lethal 18,19 screen to identify small molecules that are selectively cytotoxic to cells that have lost the VHL tumor suppressor gene.20 Subsequently, we have screened several diverse chemical libraries and identified a number of "hits". Hit compounds were validated in a growth inhibition assay and the most promising compounds were further characterized by clonogenic survival assays. We demonstrated the pyridylanilinothiazole (PAT) chemotype (Figure 1) to be active in this context and found that compounds of this chemotype induced autophagy in both cell lines, but which led to cell death in a VHL-dependent fashion.21 The lead molecule, STF-62247 (11) (Table 1), reduced tumor growth in vivo in VHL-deficient RCC compared to genetically matched cells that express wild-type VHL.21</p><p>In this study, we have synthesized a range of analogues (1–106) with substituents on each ring of the PAT chemotype as well as modifications to the linker units between the three domains. We have examined their in vitro activity as VHL-selective cytotoxins using paired renal cell carcinoma cell lines; the VHL-null cell line RCC4 and the matched line RCC4-VHL, which has VHL function restored. These well characterised cell lines are isogenic with the exception of VHL status. 8 The selectivity of the analogues was determined as the ratio of RCC4-VHL GI50/RCC4 GI50. We have examined the structure-activity relationships (SAR) for VHL-selective cytotoxicity. A quantitative analysis of these SAR was used to develop a common molecular alignment for VHL-selective members of the chemotype and this alignment was used to predict cytotoxicity and assessed as a tool to guide further analogue synthesis. Initial attempts to use this tool to direct synthesis are reported.</p><!><p>Initially, we synthesized a set of analogues (1–45) with substituents on the aniline ring (Tables 1 and 2). These analogues were conveniently prepared using the Hantzsch thiazole synthesis, condensing pyridylbromoketones with phenylthioureas (Scheme 1). 4-Pyridyl-2-bromoethanone 109 was readily prepared from 4-acetylpyridine using Br2 in HBr/HOAc. Thioureas 110–152 were commercially available or were prepared from the corresponding aniline. Direct reaction of the appropriate aniline and NH4SCN in acidic solution readily provides thioureas, albeit in low to moderate yields. For less accessible (or more expensive) anilines, reaction of benzoyl isocyanate and aniline to give corresponding benzoyl thioureas, followed by hydrolysis provided higher yields.22 Elaboration of the primary alcohol 25 to the dimethylamine 26, and reduction of the nitroaniline 31 to aminoaniline 32, was accomplished using standard chemistries (Scheme 2).</p><p>Modification of the linker between the thiazole and aniline rings was examined. Alkylation at the 2-amino position of 11 gave the 2-alkylaminothiazoles 46–48 (Scheme 3). Reaction of bromoketone 109 with thiourea gave the 2- aminothiazole 153, which was reacted with a series of acid chlorides to give the amides 49–52. Reductive amination of 153 with 3-methylbenzaldehyde gave the secondary amine 53.</p><p>Bromination of 4-pyridylpropanone gave the bromide 154, which was coupled with thioureas 120 and 144 to give 5-methylthiazoles 54 and 55, respectively (Scheme 4). Formylation of pyridylthiazoles (1, 11, 24 and 37) gave the corresponding 5-hydroxymethyl analogues 56–59. Oxidation of hydroxymethylthiazole 57 gave aldehyde 60, which underwent Wittig reaction to give a mixture of E and Z isomers of the unsaturated ester 61 (Scheme 5). Reduction of 61 gave the ester 62, which was hydrolysed to the acid 63 and then reduced to the propanol 64. Mesylation and reaction with morpholine gave the morpholide 65. The hydroxymethylthiazole 57 was further elaborated to a series of solubilised thiazole analogues 66–69 (Scheme 6). Bromination of ethyl isonicotinoylacetate gave the bromoketoester 155 which was condensed with thioureas 120 and 144 to give 5-ethylesters 70 and 71, respectively (Scheme 7). Hydrolysis of ester 70 and coupling with a variety of amines gave the amides 73–76.</p><p>Isomeric 2- and 3-pyridyl analogues 77–82 were readily prepared by reaction of the bromides 156 and 157 with thioureas 110, 120 and 130 (Scheme 8). Modification of the linker between the pyridine and thiazole rings was examined. The bromides 160 and 163 could be conveniently prepared from the 2- and 3-pyridylethanones by an extension of a regioselective bromination/debromination strategy.23 Conversion of 3- or 4-pyridine acetic acid to their Weinreb amides, 158 and 161, and then to the corresponding methyl ketones, 159 and 162, with subsequent bromination and condensation with thiourea 120 gave pyridylmethylthiazoles 83 and 84 with extended linker chains.</p><p>Finally, we sought to elaborate the pyridine ring to explore the SAR for this domain. Thus, reaction of amine 11 with MCPBA gave the N-oxide 85 (Scheme 9). In most instances preparation of the Weinreb amides of 4-pyridine carboxylic acids and Grignard reaction with MeMgBr gave 4-ethanones,24,25 which were brominated and condensed with 120 to give the corresponding PATs (Schemes 9 and 10). The 2-methoxypyridine acid was converted to the acid chloride and treated with TMSCH2N2 and the intermediate diazoketone was treated with HBr to give the bromoketone 164 (Scheme 9). The 2-Me analogue 167 was obtained by reaction of 2-picoline N-oxide with Me2SO4 and KCN to give the nitrile 165. Grignard reaction gave the ketone 166 which was brominated to give 167. Elaboration of the 2-Br PAT 90 using Stille chemistry [Pd(PPh3)4, allyltributyltin] proved to be unsuccessful, but the application of Sonogashira chemistry was effective. Thus, reaction of bromide 90 with TMS-acetylene in the presences of PdCl2(PPh3)2 and CuI, followed by removal of the TMS protecting group with TBAF, gave the 2-alkyne 92 in moderate yield. Reduction of the acetylene group gave the 2-ethyl analogue 93. A similar sequence with propargyl alcohol gave the 2-substituted propynol 94 and the corresponding propanol 95. A series of 3-substituted pyridines 96–100 were synthesized via Weinreb amide chemistry (Scheme 10). The 3-nitro PAT 100 was reduced to the 3-amino PAT 101 with subsequent acetylation giving acetamide 102. Sonogashira chemistry was used to elaborate the 3-bromo PAT 99 to a series of 3-alkynyl and 3-alkyl PATs 103–106.</p><p>In preliminary experiments to explore modelling predictions, we synthesized two additional analogues. Songashira reaction of bromide 99 gave the methyl ether 107 while Suzuki reaction of bromide 99 gave the phenyl ketone 108.</p><!><p>A minimum energy conformation for 11 was obtained using the OMEGA2 package (Openeyes), with default settings. The mmff94s force field was used for both construction and torsion driving, while the RMS torsion driving parameter was set at 0.6. All other structures were generated from this conformation using the SKETCHER module in SYBYL8.0 (Tripos) and minimized using MAXMIN2, with the Tripos force field and Gasteiger Huckel charges. Minimization was performed using 1000 steps of step descents followed by conjugate gradients until convergence at the 0.05 kcal/(mol*A) level. A distance dependent dielectric function was used with a dielectric constant of 80. Where the compound could have more than one substitution pattern, all conformers were constructed. Molecules were superimposed based on overlap of molecular volume using the ROCS alignment package (Openeyes) at default settings.</p><!><p>A Comparative Molecular Field Analysis (CoMFA) 26 3D-QSAR method was used to determine a relationship between the compounds tested and in vitro cytotoxicity. Briefly, CoMFA was performed using a cubic lattice extending 4 Å around the aligned molecules with a point spacing of 2 Å. A distance dependent dielectric along with cutoffs of 30 kcal/mol and smooth transition were used for both steric and electrostatic energy calculations. A C.3 atom with charge +1 was used as the probe. The partial least squares (PLS) regression analysis was performed using the QSAR module, with the optimum number of components extracted from the Standard Error of Predictions as determined using the SAMPLS protocol with Leave-One-Out cross validation. The optimum number of components was used in the conventional non-validated PLS analysis. Only compounds that had both GI50 and cytotoxicity ratios and substitutions up to 1 rotatable bond were used (41 compounds see Supporting Information for set).</p><!><p>Growth inhibition was determined by GI50 assays, using a 4 day drug exposure of RCC4 and RCC4/VHL cells in 96-well plates as described previously.21 The selectivity ratio was calculated as the intra-experiment ratio RCC4-VHL/RCC4 (Tables 1–5). Selected compounds (11, 37, 98, and 105) were tested in a clonogenic survival assay to assess their ability to kill RCC4 and RCC4/VHL cells in vitro. 300 cells were plated in 60 mm dishes and allowed to attach overnight. The next day, cells were treated with different concentrations of drug and colonies were stained 10 days later. These compounds were also examined for their ability to induce formation of intracytoplasmic vacuoles, thus cells were incubated with drug (5 μM) for 24 h before phase contrast images were taken.</p><!><p>We have prepared a set of PAT analogues (1–106) designed to explore the SAR for each of the domains of the chemotype. Thus, a range of substituents on each of the aniline, thiazole and pyridyl, rings were synthesized, as well as analogues with modified linkers between the three rings. The ability of these analogues to inhibit cell growth in a VHL-dependent manner was investigated by determining the GI50 values against a pair of renal cell carcinoma cell lines; the VHL-null cell line RCC4 and the matched line RCC4-VHL, which has VHL function restored. The selectivity of the analogues was determined as the ratio of RCC4-VHL GI50/RCC4 GI50. In many instances poor aqueous solubility prevented the determination of a GI50 value against the RCC4-VHL cell line, leading to a greater than value being expressed for the selectivity ratio. In the instances where inequalities were obtained for both cell lines the ratio was not determined.</p><p>The parent compound 1 was modestly potent with a GI50 of 7 μM and selectivity for the VHL-negative RCC4 cell line of >10-fold (Table 1). Addition of substituents to the 2-position of the aniline ring (2–8) was associated with a loss of potency and selectivity. Compounds with small, lipophilic substituents at the 3-position, such as the initial lead 11 with a 3-Me substituent, were active against the RCC4 cell line with low micromolar cytotoxicity and 10 to 20-fold selectivity. Increasing steric bulk in the 3-position (e.g., 12 through 14) was associated with a loss of potency and selectivity for RCC4. Polar substituents (e.g., 18–20) resulted in inactive compounds. A similar theme was observed at the 4-position, where compounds with small lipophilic substituents such as 4-Me 24 and 4-F 27 had low micromolar potency, but increasing polarity at this position was associated with a loss of activity (e.g., 29–31). Although an extended neutral side chain was tolerated in compound 25, more polar analogues with basic amine side chains (23, 26) were less potent and not selective.</p><p>The SAR for multiply-substituted anilines (33–45) mirrored that seen for single substituents (Table 2). 2,6-Disubstitution was not tolerated, whereas dialkyl substituted compounds spanning the 3-, 4- and 5-positions (35–37) had similar potencies to their mono-substituted counterparts, but displayed lower selectivity. More polar combinations (38–45) resulted in diminished cytotoxic potency and a loss of selectivity.</p><p>Replacement of the aniline NH with an N-alkyl substituent (46–48) or conversion to an amide (49–52) or benzylamine (53) consistently abolished activity suggesting a key binding interaction for the aniline NH (Table 3).</p><p>We next focussed on substituents at the 5-position of the thiazole ring (Table 4). Although small alkyl substituents (54–59) gave compounds with only slightly reduced cytotoxic potency, they suffered a complete loss of selectivity. Longer chain alkyl substituents with terminal polar groups (61–69) generally allowed retention of cytotoxic potency, but resulted in low selectivity suggesting off-target activity. Analogues with more polar ester or amide substituents (71, 73–76) were generally neither potent nor selective. Thus, substitution on the thiazole ring was not a fruitful endeavour.</p><p>Regioselectivity in the pyridine ring was explored with a series of 2- and 3-pyridyl analogues (77–82) (Table 5). These were all inactive as were 3- and 4-pyridyl analogues (83, 84) with a methylene spacer to the thiazole ring. Masking the 4-pyridyl moiety as the N-oxide (85) also ablated activity. Collectively, these data point to a key binding interaction for the 4-pyridyl moiety. Halide substituents at the 2-position of the pyridyl ring (88–91) gave potent analogues with low selectivity. Although the 2-methyl analogue 86 was inactive, higher analogues (93, 95) were potent and selective compounds. Incorporation of the acetylene unit (e.g., 92 and 94, respectively) resulted in compounds with lower potency and a loss of selectivity. The 3-halo substituted analogues (97–99) were potent and selective analogues whereas more polar substituents (100–102) resulted in lower potency and a loss of selectivity. The 3-alkyl substitutions (96, 104, and 106) generated good potency and modest selectivity and, interestingly, the inclusion of an acetylene unit (103, 105) resulted in a clear increase in cytotoxic potency and selectivity.</p><!><p>Collectively, the SAR data provided inferences for further analogue development, but in the absence of information on the molecular target of the chemotype we sought to generate a more complete description of a possible bioactive conformation for the PAT chemotype by using CoMFA to assess the relationship between structure and differential cell killing ability using VHL selectivity.</p><p>Alignments that reflected the conformer possibilities for the substitutions present in the set of compounds used for model development were tested. The data for the best model is presented in Table 6, and the putative bio-active conformation shown in Figure 2 along with steric (2a) and electrostatic (2b) field contours. Although the data are limited in the GI50 range they cover, and the low q2 value indicates that the predictive value of this model is also limited, it does provide some support for a relationship between this conformation of the PAT core and cytotoxicity, and indicates that steric fields account for 65.6% of the variation in the data while electrostatic fields explain 34.4%</p><p>Figure 2 shows that, within the model development compound set, the contouring around the aniline ring is more complex than around the pyridine ring. A large blue contour around the 3-position of the aniline ring indicates that electrostativ effect around this site is favored, while it is disfavoured around the 4- and 5-positions. Only a region close to the 5-position of this ring reported a positive effect on GI50 for steric bulk, while additional steric bulk around the 4-position is likely to have a negative effect. Compounds 23, 25 and 26 were not included in the QSAR analysis due to their flexibility; however they probe this region with both steric bulk and electrostatic properties. The GI50 values for the basic compounds increase, a result in part consistent with the disfavored electrostatic contour around this site; by contrast the smaller alkyl hydroxyl side chain is accepted at this position with only a modest loss of activity, also supporting the yellow steric contour. Strikingly, the contour maps report the positive effect of steric bulk at the 3-position of the pyridine ring, while electrostatic effects around this region are likely to have a negative effect on GI 50.</p><p>Maintaining or increasing the selective cytotoxicity for RCC4 is important to the development of this series of compounds, thus we overlaid those compounds with ratios of 10 or more (including 12, ratio 9.6) (Figure 2). Features common to compounds with high selectivity include the positive steric contour, green volume, at the pyridine ring 3-position while avoiding interaction with an adjacent disfavoured electrostatic red region. In addition, selective compounds also had increased steric bulk around the 4- and 5- positions of the aniline ring while avoiding an interaction with the disfavoured electrostatic region at the aniline 3-and 4-positions. Substituents on the pyridine ring provide the greatest potential for the definition of a new ligand domain.</p><p>We then tested the ability of the alignment to guide synthesis by exploring the steric pocket adjacent to the 3-position of the pyridyl ring. Two simple analogues of the existing series were prepared. Thus, synthesis of the 3-propargyl methyl ether 107 was achieved using a Sonogashira reaction with bromide 99 (Scheme 10). Similarly, Suzuki coupling of bromide 99 with 4-acetylphenylboronic acid gave the ketone 108. The ether 107 retained VHL cytotoxic potency [GI50 (RCC4) 0.62 μM] and was more selective (45-fold) when compared to the propargyl alcohol 105 (11-fold), confirming the potential use of the steric pocket to access improved PAT analogues. The use of a phenyl ring to probe the steric space was less successful with 108 displaying low micromolar potency [GI50 (RCC4) 3.9 μM] and modest selectivity (9-fold). The presence of this steric pocket may be useful when designing affinity chromatography reagents suitable for protein purification and identification studies.</p><p>We evaluated several of the more active compounds from the SAR set to confirm their mechanism of action was the same as the initial lead 11. Compounds 37, 98 and 105 were tested for their ability to suppress clonogenic survival and were shown to selectively kill RCC4 cells compared to RCC4/VHL (see Supporting Information for survival curves). Compounds 37, 98, 105 and 107 were also examined for their ability to induce autophagy (Table 7). Treatment with the compounds (5 μM) for 24 h initiates the formation of intracytoplasmic vesicles in a similar manner to 11, which in combination with the clonogenic data confirms the mode of action for these analogues as VHL-selective induction of autophagy resulting in cell death.</p><!><p>We have synthesized an exploratory SAR compound set to investigate the chemical space around the PAT chemotype. Empirical observation identified several key features necessary for selective cytotoxicity against VHL-negative renal carcinoma cells. The aniline-NH and the 4-pyridyl-N are likely to be involved in hydrogen bonding to the as yet undetermined molecular target, while an unsubstituted thiazole is required for VHL selectivity. The activities of compounds with small lipophilic substituents at the 3- and 4-positions of the aniline ring are suggestive of the presence of a lipophilic pocket in the molecular target. A subset of VHL-selective compounds was used to create a molecular alignment to further explore the chemotype and develop a predictive model. CoMFA analysis suggested the alignment had low predictive power; however the alignment did consistently interpret all the data. The alignment model also suggested the presence of a steric pocket adjacent to the 3-position of the pyridine ring that might provide a new domain for analogue development. Preliminary efforts to explore this pocket were successful with two analogues displaying increased VHL-selective cytotoxicity. The activity of these additional analogues demonstrates the potential of the alignment to identify new domains to explore in the search for more potent and selective VHL-dependent cytotoxins. Further studies are currently underway to utilise the QSAR around this chemotype to improve potency and selectivity, as well as to develop tools to explore the novel mechanism of action of the class. This will enable further development of this novel targeted approach to the treatment of Renal Cell Carcinoma.</p><!><p>General experimental details are described in the Supporting Information. All final products were analysed by reverse-phase HPLC, (Altima C18 5 μm column, 150 × 3.2 mm; Alltech Associated, Inc., Deerfield, IL) using an Agilent HP1100 equipped with a diode-array detector. Mobile phases were gradients of 80% acetonitrile/20% H2O (v/v) in 45 mM ammonium formate at pH 3.5 and 0.5 mL/min. Purity was determined by monitoring at 330 ± 50 nM and was >95% in all cases.</p><!><p>See Supporting Information for full experimental details.</p><!><p>Br2 (80 mmol) was added dropwise to a stirred a solution of acetylpyridine (80 mmol) in 30% HBr/HOAc (100 mL) at 15 °C. The mixture was stirred at 40 °C for 1 h and then 75 °C for 1 h. The mixture was cooled to 20 °C, diluted with Et2O (400 mL) and stirred for 30 min. The precipitate was filtered, washed with Et2O (25 mL) and dried under vacuum to give the bromoethanone as the hydrobromide salt.</p><!><p>NH4SCN (50 mmol) was added to a stirred solution of m-toluidine (50 mmol) in 1 M HCl (50 mL) at 100 °C and the solution stirred at 100 °C for 16 h. The solution was diluted with water (60 mL) and stood at 5 °C for 2 h. The precipitate was filtered, washed with water (5 mL), washed with ether (5 mL), and dried. The precipitate was purified by column chromatography, eluting with an appropriate blend (30–100%) of EtOAc/pet. ether, to give the thiourea.</p><!><p>Benzoyl chloride (65 mmol) was added dropwise to a solution of NH 4SCN (69 mmol) in dry acetone (50 mL). The mixture was stirred at reflux temperature for 15 min. The heating was removed and m-toluidine (46 mmol) was added dropwise keeping the solution at reflux. The mixture was stirred at reflux temperature for a further 30 min, cooled to 20 °C and poured onto ice. The mixture was stirred for 30 min and then the precipitate was filtered and washed with water (15 mL) and dried. The solid was added to a solution of NaOH (10% w/v, 100 mL) at 80 °C and stirred at 80 °C for 30 min, then cooled to 20 °C and poured onto ice/HCl (6 M, 50 mL). The pH of the mixture was adjusted to 10 with cNH3 solution and stirred for 30 min. The precipitate was filtered and washed with water (20 mL) and dried. The precipitate was purified by column chromatography, eluting with an appropriate blend (30–100%) of EtOAc/pet. ether, to give the thiourea.</p><!><p>A mixture of bromoketone hydrobromide (3 mmol) and phenylthiourea (3 mmol) in EtOH (20 mL) was stirred at reflux temperature for 1 h. The mixture was cooled to 20 °C, diluted with water (50 mL), the pH adjusted to ca. 8 with aqueous NH3 and the mixture stirred at 20 °C for 2 h. The precipitate was filtered, washed with water (5 mL) and dried. The solid was purified by column chromatography, eluting with an appropriate blend (30–100%) of EtOAc/pet. ether, to give the thiazole.</p><!><p>Et3N (6.0 mmol) was added to a stirred suspension of 4-pyridinylacetic acid (1.5 mmol), EDCI (1.7 mmol), HOBT·H2O (1.7 mmol) and MeNHOMe·HCl (2.3 mmol) in dry DCM (50 mL), and the mixture was stirred at 20 °C for 16 h. The resulting solution was diluted with DCM (100 mL) and washed with water (2 × 30 mL), washed with brine (30 mL), dried and the solvent evaporated. The residue was purified by column chromatography, eluting with a gradient of an appropriate blend (0–10%) of MeOH/EtOAc, to give the amide.</p><!><p>A solution of MeMgBr (3 M in hexanes, 7.5 mmol) was added slowly to a stirred solution of amide (5 mmol) in dry THF (50 mL) at 0 °C and the mixture was stirred at 0 °C for 8 h. The reaction mixture was quenched with saturated aqueous NH4Cl solution (20 mL) and the mixture extracted with EtOAc (3 × 50 mL). The combined organic fraction was washed with water (40 mL) washed with brine (40 mL), dried and the solvent evaporated. The residue was purified by column chromatography, eluting with 30% EtOAc/pet. ether, to give ketone.</p><!><p>GI50 values for compounds were determined by XTT assay. For 2,3-bis[2-methoxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide inner salt (XTT) assays, five thousand cells were plated in 96-well plates. The next day, vehicle or drug was added to each well and incubated for four days. Media was aspirated and phenol red-free medium with 0.3 mg/mL XTT (Sigma Chemical Co) in Phenol Red-free media, 20% FCS and 2.65 ug/mL N-methyl dibenzopyrazine methyl sulfate was added. The cells were incubated at 37 °C for 1–2 hours and absorbance was read at 450 nm. GI50 values for each compound were calculated using linear interpolation.</p><!><p>Three hundred cells were plated into 60-mm tissue culture dishes in DMEM. The next day, cells were treated with vehicle or drug and were further incubated for an additional 10 days. After 10 days, the media was removed and colonies were fixed and stained in 95% ethanol and 0.1% crystal violet for 15 minutes. The stain was removed and plates were washed in deionized water. Colonies were quantified. All conditions were measured in triplicate and all experiments were performed in triplicate.</p><!><p>Figure 2(a): 3D-QSAR conformer model relating PAT conformation to cytotoxicity. Electrostatic fields are contoured at 80% favoured (blue) and 20% disfavoured (red); (b) Steric fields are contoured at 80% favoured (green) and 20% disfavoured (yellow).</p><p>aReagents: (i) Br2, HOAc/HBr; (ii) NH4SCN, aqueous HCl; (iii) PhCOCl, NH4SCN, acetone; then aqueous NaOH; (iv) EtOH. $ = commercially available.</p><p>aReagents: (i) MsCl, iPr2NEt, DCM; (ii) Me2NH, DMF; (iii) H2, Pd/C, EtOH</p><p>aReagents: (i) NaH, RI, DMF; (ii) NH2CSNH2, EtOH; (iii) benzoic acid, (COCl)2, DMF, DCM; (iv) 3-methylbenzaldehyde, THF; then NaBH4, H2O.</p><p>aReagents: (i) Br2, HOAc/HBr; (ii) EtOH; (iii) HCHO, Et3N, THF. $ = commercially available.</p><p>aReagents: (i) MnO2, benzene; (ii) Ph3P=CHCO2Me, DCM;</p><p>(iii) H2, Pd/C, EtOH, EtOAc; (iv) NaOH, EtOH; (v) LiAlH4, THF; (vi) MsCl, iPr 2NEt, DCM; (vii) morpholine, DMF.</p><p>aReagents: (i) MsCl, iPr2NEt, DCM; (ii) amine, DMF.</p><p>aReagents: (i) Br2, CHCl3; (ii) EtOH; (iii) NaOH, EtOH; (iv) (COCl)2, DMF, DCM; (v) amine, DCM. $ = commercially available.</p><p>aReagents: (i) Br2, HOAc/HBr; (ii) Arylthiourea, EtOH; (iii) MeNHOMe, EDCI, HOBT, Et3N, DCM; (iv) MeMgBr, THF. $ = commercially available.</p><p>aReagents: (i) MCPBA, DCM; (ii) (COCl)2, DMF, DCM; (iii) TMSCH2N2, THF; then HBr; (iv) Arylthiourea, EtOH (v) Me2SO4, then KCN, aq. EtOH; (vi) MeMgBr, THF; (vii) Br2, HOAc/HBr; (viii) Me(OMe)NH·HCl, EDCI, HOBT, Et3N, DCM; (ix) PdCl2(PPh3)2, CuI, TMSC≡CH, Et3N, DMF, then TBAF; (x) H2, Pd/C, EtOH; (xi) PdCl2(PPh3)2, CuI, HC≡CCH2OH, Et3N, DMF. $ = commercially available.</p><p>aReagents: (i) Me(OMe)NH·HCl, EDCI, HOBT, Et3N, DCM; (ii) MeMgBr, THF; (iii) Br2, HOAc/HBr; (iv) 3-methylphenylthiourea 118, EtOH; (v) H2, Pd/C, EtOH; (vi) Ac2O, dioxane; (vii) PdCl2(PPh3)2, CuI, TMSC≡CH, Et3N, DMF, then TBAF; (ix) PdCl2(PPh3)2, CuI, HC≡CCH2OH, Et3N, DMF; (x) PdCl2(PPh3)2, CuI, HC≡CCH2OMe, Et3N, DMF; (xi) PdCl2dppf, K2CO3, CH3COPhB(OH)2, toluene, EtOH, H2O, DMF. $ = commercially available.</p><p>GI50 values and selectivity ratios for substituted 4-PATs</p><p>Single determinations in triplicate;</p><p>Ratio = RCC4-VHL GI50/RCC4 GI50;</p><p>nd, not determined due to low solubility;</p><p>nt, not tested.</p><p>GI50 values and selectivity ratios for substituted 4-PATs</p><p>Single determinations in triplicate;</p><p>Ratio = RCC4-VHL GI50/RCC4 GI50;</p><p>nd, not determined due to low solubility;</p><p>nt, not tested.</p><p>GI50 values and selectivity ratios for linkers</p><p>Single determinations in triplicate;</p><p>Ratio = RCC4-VHL GI50/RCC4 GI50;</p><p>nd, not determined due to low solubility.</p><p>GI50 values and selectivity ratios for thiazole substituents</p><p>Single determinations in triplicate;</p><p>Ratio = RCC4-VHL GI50/RCC4 GI50;</p><p>nd, not determined due to low solubility;</p><p>nt, not tested.</p><p>GI50 values and selectivity ratios for A ring substituents</p><p>Single determinations in triplicate;</p><p>Ratio = RCC4-VHL GI50/RCC4 GI50;</p><p>nd, not determined due to low solubility;</p><p>nt, not tested.</p><p>Statistical analysis of the QSAR model.</p><p>Induction of autophagy by PATs in RCC4 cells.</p>