Poorly vascularized areas of solid tumors contain quiescent cell populations that are resistant to cell cycle-active cancer drugs. The compound VLX600 was recently identified to target quiescent tumor cells and to inhibit mitochondrial respiration. We here performed gene expression analysis in order to characterize the cellular response to VLX600. The compound-specific signature of VLX600 revealed a striking similarity to signatures generated by compounds known to chelate iron. Validation experiments including addition of ferrous and ferric iron in excess, EXAFS measurements, and structure activity relationship analyses showed that VLX600 chelates iron and supported the hypothesis that the biological effects of this compound is due to iron chelation. Compounds that chelate iron possess anti-cancer activity, an effect largely attributed to inhibition of ribonucleotide reductase in proliferating cells. Here we show that iron chelators decrease mitochondrial energy production, an effect poorly tolerated by metabolically stressed tumor cells. These pleiotropic features make iron chelators an attractive option for the treatment of solid tumors containing heterogeneous populations of proliferating and quiescent cells.
Iron is an essential nutrient that enables a plethora of biological processes including DNA replication and mitochondrial respiration. Cancer cells display increased rate of iron uptake and usage1. Thus, iron may have an even more fundamental role in tumor cell hemostasis than is generally appreciated. Ferrous iron is present in a cytoplasmic pool of soluble and chelatable iron, i.e. the labile iron pool1. Increases in the size of the labile iron pool has been reported to lead to increased tumor cell proliferation2. Iron is a necessary component of haem and iron-sulfur clusters, present in enzymes involved in oxidative phosphorylation (OXPHOS) and the Krebs cycle3. Iron is also required for the enzymatic activity of ribonucleotide reductase (RR), catalyzing the conversion of ribonucleotides to deoxyribonucleotides4. Indeed, several iron chelators have been shown to possess anti-cancer activity1,5,6,7,8,9.
We recently identified the small molecule VLX600 (Fig. 1A) as a candidate drug that preferentially targets quiescent cells in colon cancer 3-D multicellular tumor spheroids (MCTS)10. Similar to other compounds targeting quiescent cells in MCTS11,12, VLX600 affects mitochondrial function. The anti-cancer activity of VLX600 is attributed to the limited metabolic plasticity of cancer cells in hypoxic and nutritionally compromised environments, in which cells are unable to compensate for decreased mitochondrial OXPHOS by other means of energy production. This ultimately leads to a bioenergetic catastrophe and tumor cell death13.
In contrast to other agents that decrease the viability of MCTS such as nitazoxanide11, VLX600 also inhibits the proliferation of tumor cells in 2-D monolayer culture10. This observation prompted us to investigate the molecular mechanism of action of VLX600. We here report that VLX600 binds iron and that this property is the underlying mechanism of the ability of VLX600 to reduce cell proliferation and to decrease mitochondrial OXPHOS. We show that also other iron chelators have the ability to affect the viability of MCTS, albeit with lower potency than VLX600. The ability of iron chelators to reduce mitochondrial energy production adds to the evidence of this class of compounds as having attractive anti-neoplastic activities.
VLX600 is an iron chelator
The molecular structure of VLX600 is shown in Fig. 1A. The precise molecular mechanism of action of VLX600 was unknown and we therefore performed a Connectivity Map-based mechanistic exploration by examining the gene expression profile of drug-treated tumor cells14. We employed two different cellular models; the breast cancer cell line MCF-7 and colon carcinoma cell line HCT116, grown as 2-D monolayer and 3-D MCTS, respectively. MCF-7 cells were chosen since it is the most frequently used cell model in the Connectivity Map database. We selected MCTS HCT116 to investigate if the response is the similar when cells were grown in 3-D cell culture. The gene expression signature induced by VLX600 was most similar to that of ciclopirox olamine (CPX; 6-cyclohexyl-1-hydroxy-4-methyl-2(1H)-pyridone 2-aminoethanol), the ChemBridge compound 5109870 (2-hydroxy-3-methoxybenzaldehyde 2-pyridinylhydrazone), and deferoxamine (Fig. 1B). All of these compounds were previously described as iron chelators15,16,17, suggesting that the anticancer activity of VLX600 could be attributed to iron chelation and sequestering. Complex formation between VLX600 and different metals was examined using spectrophotometry (Fig. 1C). VLX600 was indeed found to form complexes with ferrous and ferric iron as well as with Co2+, whereas only minor changes in the UV/Vis spectra were observed with Cu2+, Zn2+, Ni2+ or Al3+ (Fig. 1C). Addition of extracellular iron (Fe2+ and Fe3+) abolished the cytotoxic activity of the compound (Fig. 1D), supporting the hypothesis of iron chelation being instrumental to biological activity of VLX600. As previously described, VLX600 is able to reduce mitochondrial OXPHOS, particularly uncoupled respiration10. We found that addition of iron chloride restored OXPHOS capacity in cells exposed to VLX600 (Fig. 1E).
Characterization of iron chelation
By means of density functional theory (DFT) calculations on Fe(II)(VLX600)2, the N2 nitrogen in the 1,2,4-triazine moiety was found to preferentially coordinate iron over the N4 nitrogen by as much as 18 kcal/mol (Fig. 2A). Using this coordination mode, the geometries were calculated for both oxidation states and spin states of Fe(VLX600)2 (Supplementary Table 1). Extended X-Ray Absorption Fine Structure (EXAFS) confirmed that iron(II) binds two VLX600 ligands to form a bis-complex where iron binds six nitrogen atoms in a pseudo-octahedral configuration at very short Fe-N bond distances, 1.90 and 1.915 Å for iron(II) and iron(III), respectively. This is in good agreement with reported iron(II)-terpyridine complexes, Supplementary Table 3 and the DFT calculated distances. Furthermore, Fe-C/N distances at ~2.80, 3.35 and 4.05 Å were identified and fit with distances observed in the iron(II)-terpyridine complexes and those in the calculated model presented in Fig. 2A. The very short Fe-N bond distances are consistent with both iron(II) and iron(III) being present as low-spin complexes, and with significant back-bonding for iron(II) making the bond distances even shorter and the complex being significantly stabilized. The refined structure parameters are given in Supplementary Table 2, and the model fits of the experimental EXAFS and corresponding Fourier transforms (Supplementary Figures 1 and 2, respectively). The positions of the absorption edges clearly show that the VLX600 complexes of both iron(II) and iron(III) in principle remain in their oxidation states after 48 hours of storage, see Figure S3. The iron(III) complex seems to be completely stable, while there is maybe a sign that the iron(II) complex is partly oxidized as seen in the slightly longer mean Fe-N bond distance (Supplementary Table 2), and the somewhat different shape of the absorption edge, see Figure S3. The pre-edge at 7111–7114 eV is a strong indicator of the oxidation state of iron18. However, in these cases the pre-peak is observed at 7112 eV for both complexes, likely due to that they are low-spin complexes and with significant back-bonding in the iron(II) VLX600 complex, Figure S3.
The chemical structure of VLX600 was modified by altering the position of the nitrogen in the pyridine moiety (VLX641 and VLX642; Fig. 2B). According to the model describing the coordination mode (Fig. 2A), this modification would result in loss of tridentate iron binding and, thus, biological activity of the molecules. Indeed, the VLX600 analogues showed no cytotoxic activity (Fig. 2C), suggesting limited off-target effects of the molecular scaffold in this biological system. Furthermore, the chemical alterations abolished the effect on mitochondrial respiration (Fig. 2D).
Inhibition of tumor cell proliferation by VLX600
VLX600 was identified in a screen for compounds active on 3-D tumor spheroids but also shows antiproliferative activity on colon cancer cell lines in monolayer culture10. We examined the effect of VLX600 on a number of colon cancer cell lines and generally found IC50 values in the order of 1 μM (Fig. 3A–G). VLX600 was more potent than other iron chelators (i.e. Triapine (3-aminopyridine-2-carboxaldehyde-thiosemicarbazone)8, CPX, VLX5019, and deferoxamine) (Fig. 3A–G). DNA synthesis of colon cancer cells grown in monolayer culture was inhibited as evidenced by decreased incorporation of 5-ethynyl-2′-deoxyuridine (EdU) (Fig. 3H,I). The catalytic activity of ribonucleotide reductase is dependent on an iron-binding site in the M2 subunit of the enzyme and iron chelators have been found to inhibit this enzyme20. As expected, VLX600 inhibited ribonucleotide reductase activity in vitro (Fig. 3J).
Inhibition of mitochondrial activity and spheroid viability by iron chelators
We examined whether also other iron chelators have the ability to decrease mitochondrial oxygen consumption. Indeed, CPX, Triapine and deferoxamine all decreased uncoupled OXPHOS (Fig. 4A). CPX and Triapine reduced HCT116 MCTS viability (i.e. GFP signal; previously validated to be a reliable surrogate marker of viability11), although with considerably lower potency compared with VLX600 (Fig. 4B). MCTS formed from HT-29 were only affected by VLX600 and higher concentrations of Triapine whereas deferoxamine did not show detectable activity even at concentrations >300 μM. Compound lipophilicity is particularly important for activity in MCTS systems21 as well as in solid tumors in vivo22. The higher 3-D cytotoxic potency of VLX600 compared to other iron chelators examined here may at least be partially explained by the higher lipophilicity of VLX600 (XlogP ~ 3) (Supplementary Table 4).
Decreased hypoxia in spheroids and in tumors
The level of oxygen consumption in spheroids is expected to be reflected in the degree of hypoxia10. Exposure of spheroids to a mitochondrial uncoupler does indeed increase the pimonidazole hypoxic fraction (pHF) whereas VLX600 decreases the pHF (Fig. 5A). Similar to VLX600, ciclopirox reduced the pHF, albeit to lower degree than VLX600 (Fig. 5A), whereas deferoxamine did not cause any observable effect (Fig. 5A). These alterations of pHF are consistent with the observed degree of changes in MCTS viability (Fig. 4B).
VLX600 is well tolerated by rodents and shows anti-tumor activity in animal tumor models which are associated with decreased proliferative indices10. To address the question whether VLX600 affects tumor hypoxia in vivo, we injected VLX600 into mice bearing HCT116 colon cancer xenografts. VLX600 exposure significantly reduced the pHF 4 hours after injection of the drug (Fig. 5B,C).
VLX600 decreases cytochrome oxidase activity in spheroids
We and others have hypothesized that energy production in tumor cells situated in the deep tumor parenchyma is vulnerable and cannot tolerate even limited decreases in OXPHOS10,11,12,13. OXPHOS is known to be functional at oxygen concentrations as low as 0.5%23 but it is not known whether electron transport components are expressed in core regions of spheroids. Cytochrome oxidase (complex IV) is rate-limiting in the electron transport chain24 and its activity was reported to decrease under hypoxic/hypoglycemic conditions25. We examined the distribution of cytochrome oxidase IV (COXIV) immunoreactivity and cytochrome oxidase in situ activity in colon cancer spheroids (Fig. 5D). Immunoreactivity and enzymatic reactivity were strongest in the area of 50–100 μm from the spheroid surface containing Ki67-positive, proliferating cells (Fig. 5D). However, COXIV activity was clearly discerned in the core regions of the spheroids (Fig. 5D,E). Exposure to VLX600 for 24 hours led to a uniform reduction of cytochrome oxidase activity in MCTS and also to a decreased immunoreactivity for COXIV (Fig. 5D).
The cells in the cores of MCTS have the ability to regrow after cytotoxic therapy26 and have in this respect similarities to cancer initiating stem cells. Recently, several studies have identified inhibition of mitochondrial OXPHOS as a promising strategy to combat quiescent cancer cells in hypoxic and nutritionally compromised environments10,11,27,28,29. There is a growing body of observational evidence to support this idea. Importantly, and contrary to the Warburg hypothesis, mitochondria are the main source of ATP production in cancer cells30 and OXPHOS is the predominant source of ATP in also hypoxic layers of MTCS31. Furthermore, increased OXPHOS activity is observed in human tumors in situ compared with adjacent normal tissue32. Components involved in mitochondrial biogenesis, mitochondrial translation and mitochondrial lipid biosynthesis are transcriptionally upregulated in human breast cancer epithelial cells and downregulated in adjacent stromal cells33. Elevated expression of the mitochondrial markers such as TIMM17A and TOMM34 is associated with poor clinical outcome and may be predictive of higher tumor grade and metastasis34,35,36.
Mitochondrial inhibitors have long been reported to possess anti-tumor activity37,38,39. Examples of such compounds are Rho12337, which inhibits OXPHOS40, and mitochondria-targeted lipophilic cations41. Metformin is a commonly prescribed anti-diabetic drug that increases cellular glucose uptake42. Metformin inhibits mitochondrial OXPHOS, likely through inhibition of complex I activity43,44 and metformin exposure appears to diminish tumor formation in diabetic patients45 and in mouse animal models46,47. VLX600 is a mild inhibitor of OXPHOS, primarily inhibiting uncoupled respiration (i.e total respiratory capacity)10. It is interesting to note that the limited effect on OXPHOS elicited by VLX600 on monolayer cultures is associated with major effects on hypoxia in spheroids. A possible explanation for this phenomenon is that total available, albeit limited, mitochondria capacity is utilized in the cells of the core area, and that mild inhibition has large consequences in oxygen utilization and energy production.
Iron chelators have complex effects on tumor cells1,5,6,7,8,9. Inhibition of ribonucleotide reductase results in inhibition of cell proliferation by depleting deoxyribonucleotide pools and we here show that iron chelators affect OXPHOS. We previously reported that VLX600 induces HIF-1α expression10, an observation explained by the present finding that the drug chelates iron. Prolyl hydroxylases, that negatively regulates HIF-1α protein stability, are iron-dependent enzymes48 and iron chelators are known to induce HIF-1α49 VLX600 induces a HIF-1α-dependent shift to glycolysis in exposed cells10, and it is possible that this leads to further depletion of glucose in tumors and a strengthened bioenergetic catastrophe. Some iron chelators form redox-active complexes with metals, notably cupper, and this has been reported to be essential for their ability to induce apoptosis50. Hovever, exposure to VLX600 does not result in the generation of increased levels of reactive oxygen species in cells10, and the antiproliferative effects of this drug is therefore most likely due to depletion of cellular labile iron pools.
The ability of iron chelators to inhibit the proliferation and decrease the viability of heterogeneous populations of tumor cells in solid tumors opens interesting possibilities for future therapies. VLX600 is presently in a phase-I clinical trial (ClinicalTrials.gov NCT02222363) for patients with refractory advanced solid tumors which will hopefully provide proof of concept for this treatment strategy.
HCT116, HT-29, SW620, HT8, DLD, RKO and MCF-7 were obtained from the American Type Culture Collection, Manassas, VA, USA). HCT116 GFP and HT-29 GFP (human epithelial colon carcinoma cell lines constitutively expressing green fluorescent protein) were purchased from Anticancer Inc. (San Diego, CA, USA). All cell lines were sub-cultivated and grown in supplemented medium as recommended by the providers. The cell banks performed authentications by short tandem repeat analysis. No further authentication was performed in our laboratory. All experiments with purchased cell lines were performed within 6 months after resuscitation. Cells were cultured in McCoy’s 5A Modified Medium (Sigma-Aldrich) +v/v 10% inactivated fetal calf serum, antibiotics (streptomycin 50 μg/mL and penicillin 60 μg/mL) and 2 mmol/L L-glutamine at 37 °C in 5% CO2. MCF-7 cells were maintained in Minimum Essential Medium Eagle (M5650, Sigma-Aldrich, Stockholm, Sweden), supplemented with 10% heat-inactivated FCS (Sigma-Aldrich, Stockholm, Sweden), 2 mmol/L L-glutamine, 100 μg/mL streptomycin, 100 U/mL penicillin (Sigma-Aldrich, Stockholm, Sweden) and 1 mM sodium pyruvate (P5280, Sigma-Aldrich, Stockholm, Sweden).
VLX600, VLX641 and VLX642 were were acquired from OnTarget Chemistry (Uppsala, Sweden). Deferoxamine, ciclopirox and triapine were from Sigma-Aldrich (St. Louis, MO, USA). For iron chelation experiments, Cu2+, Co2+, Al3+, Ni2+, Zn2+ (nitrate salts) and FeCl2 and FeCl3 were obtained from Sigma Aldrich (St Louis, MO, USA).
The Connectivity Map (CMAP) (www.broad.mit.edu/cmap) build 02 contains genome-wide expression data for 1300 compounds (6100 instances, including replicates, different doses and cell lines). We followed the original protocol using MCF-7 breast cancer cells as described by Lamb et al.14. Briefly, cells were plated in 6-well plates at a density of 0.4 × 106 cells per well and were left to attach for 24 h prior to addition of drugs. We also performed CMAP-based mechanistic exploration in MCTS HCT116. MCTS HCT116 were grown as previously described10 and were exposed to VLX600 (10 μM) or to vehicle control (DMSO). After 6 hours treatment, the cells were washed with PBS and total RNA was prepared using RNeasy miniprep kit (Qiagen, Chatsworth, CA). Starting from two micrograms of total RNA, gene expression analysis was performed using Genome U133 Plus 2.0 Arrays according to the GeneChip Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA). Raw data was normalized with MAS5 (Affymetrix) and gene expression ratios for drug treated vs. vehicle control cells were calculated to generate lists of regulated genes. Filter criteria were present calls for all genes in both the VLX600 treated DMSO (vehicle) exposed control cells and an expression cut-off of at least 200 arbitrary expression units. Only probes present on HG U133A were used, for CMAP compatibility. The 30 most up and down regulated genes (i.e., probes) for each compound were uploaded into CMAP and compared to the 6100 instances in the CMAP database, to retrieve a ranked compound list. Raw and normalized expression data have been deposited at Gene Expression Omnibus with accession number GSE84051 (MCF-7) and GSE53777 (MCTS HCT116).
Metal chelation analysis
10 μM different metals (Cu2+, Co2+, Al3+, Ni2+, Zn2+, Fe2+ and Fe3+) were separately mixed with 10 μM VLX600. Absorbance spectra over the range 210–550 nm were obtained on Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA USA). The maximum absorption wavelength of VLX600 is 340 nm.
The Fluorometric Microculture Cytotoxicity Assay, FMCA, described in detail previously51, was used for measurement of the cytotoxic effect of library compounds and the established standard drugs. The FMCA is based on measurement of fluorescence generated from hydrolysis of fluorescein diacetate (FDA) to fluorescein by cells with intact plasma membranes. Cells were seeded in the drug-prepared 384-well plates using the pipetting robot Precision 2000 (Bio-Tek Instruments Inc., Winooski, VT). In each plate, two columns without drugs served as controls and one column with medium only served as blank. Cell viability was also monitored using the MTT assay52 (in Fig. 1D).
Spheroid viability assay
The spheroid-based cytotoxicity assay was performed as described previously11, with minor modifications. Briefly, 5,000 HCT116 GFP cells or 5,000 HT-29 GFP cells were seeded in 50 μL of McCoy’s 5A medium (10% FBS, 2 mM glutamine, 50 μg/mL streptomycin, 60 μg/mL penicillin) into each well of 384-well U-bottom Ultra Low Attachment plates (Corning, NY). After seeding, plates were centrifuged at 1,000 rpm for 5 minutes. Subsequently, spheroids were grown for 7 days without medium change in 37 °C, 5% CO2. Then, drugs were administered using Echo Liquid Handler 550 (Labcyte, Sunnyvale, CA). After 96 h of drug incubation, mean spheroid GFP fluorescence was measured using ArrayScan VTI Reader (Cellomics Inc., Pittsburgh, PA, USA).
Ribonucleotide reductase assay
Ten million (1 × 107) HCT116 cells grown in 150 mm plates were exposed to indicated drugs for 24 hours. The ribonucleotide assay was performed as previously described19.
Multicellular spheroids produced by the hanging drop method in 96 well plates were fixed in 2% buffered formalin, dehydrated, embedded in paraffin and sectioned. Each sample contained 24 spheroids (spheroids from each 96 well plate were pooled into 4 groups). The sections were deparaffinized with xylene, rehydrated and microwaved and then incubated overnight with the monoclonal primary antibodies diluted in 1% (wt/vol) bovine serum albumin and visualized by standard avidin–biotin–peroxidase complex technique (Vector Laboratories, Burlingame, CA, USA). Counterstaining was performed with Mayer’s haematoxylin. Antibody MIB-1 (against the nuclear proliferation-associated antigen Ki67) was from Immunotech SA, Marseille, France and used at a dilution 1:400.
XlogP3 values were retrieved from Pub Chem https://pubchem.ncbi.nlm.nih.gov/compound/.
Assessment of cellular DNA synthesis
The fluorescence microscope ArrayScan V HCS system (Cellomics Inc.) was used for measurement of 5-ethynyl-2′-deoxyuridine (EdU) incorporation. HCT116 cells were seeded into 96-well plates (PerkinElmer Inc., Wellesley, MA, USA), left to attach over night, before test compounds were added. Cells were treated with VLX600 for 24 h or vehicle control. Cells were stained using Click-iT EdU HCS assay (C10354, Invitrogen, Molecular Probes Inc., OR, USA) according to the manufacturer’s instructions. Processed plates were loaded in the ArrayScan and analyzed. Images were acquired for each fluorescence channel, using suitable filters with 10x objective and in each well at least 1,000 cells were analyzed. Average total intensity in the EdU channel was measured.
Measurement of oxygen consumption rates (OCR)
Measurements of cellular oxygen consumption were performed using a Seahorse XF analyzer as recommended by the manufacturer (Agilent Technologies, Santa Clara, CA). Briefly, cells were pleated in 100 μL culture medium in XF 24-well cell plates with indicated blank control wells. Plates were first placed at room temperate for 1 hour and then moved to an incubator for another 1–5 hours to facilitate attachment of cells. Another 150 μl of culture medium was then added to each well followed by overnight incubation. Before the OCR measurements, medium was removed from each well and replaced with 500 μL Seahorse assay media (pyruvate 1 mM, glucose 25 mM) at 37 °C without CO2 for 1 h. OCR were measured using an XF24 Extracellular Flux Analyzer. A cell mitochondrial stress kit from Seahorse Bioscience was used for mitochondrial stress tests and experiments were performed as described previously10.
Assessment of pimonidazole adducts accumulation in mouse xenografts
Once HCT116 tumors in SCID mice had grown to a size of 200 mm3, mice were injected with VLX600. Pimonidazole was injected 1 hour before the animals were sacrificed. Tumors were sectioned and stained for pimonidazole adducts. Quantification was performed double blind from photographs of the stained slides.
All density functional calculations were done using Jaguar 8.553 (Schrodinger, Inc., New York, NY, 2014). Structures were optimized using the LACVP* basis set54 and the M06 functional55. Single-point energy calculations were performed using the LACVP** basis set with a PBF solvation model56 for water using geometries from M06/LACVP*. C2 symmetry was used in all complexes where applicable.
IC50-values and EC50-values (inhibitory/effective concentration 50%) were calculated by using non-linear regression and a standard sigmoidal dose-response model in the GraphPad Prism program (GraphPad Software, Inc. San Diego, CA, USA). Statistical significance was assessed using Student’s t-test (Microsoft Excel).
How to cite this article: Fryknäs, M. et al. Iron chelators target both proliferating and quiescent cancer cells. Sci. Rep. 6, 38343; doi: 10.1038/srep38343 (2016).
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We are grateful to Cancerföreningen in Stockholm, Cancerfonden, Vetenskapsrådet and Barncancerfonden for support. We are grateful to Hans Rosén, Vivolux AB, for support and input at various levels as well as organizational help. We acknowledge Accelera, Milan, for performing the animal studies and OnTarget Chemistry, Uppsala, Sweden, for synthesis of compounds. We are grateful to Uppsala Array platform, Maria Rydåker, Lena Lenhammar and Christina Leek for excellent technical support. Portions of this research were carried out at beam-line I811, MAX-lab synchrotron radiation source, Lund University, Sweden. Funding for the beam-line I811 project was kindly provided by The Swedish Research Council and the Knut och Alice Wallenbergs Stiftelse.
M.F., J.G., P.N., S.L. and R.L. are minor shareholders in Vivolux AB. The remaining authors have no competing financial interests.
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Fryknäs, M., Zhang, X., Bremberg, U. et al. Iron chelators target both proliferating and quiescent cancer cells. Sci Rep 6, 38343 (2016). https://doi.org/10.1038/srep38343
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