The tumor inhibitor and antiangiogenic agent withaferin A targets the intermediate filament protein vimentin

Abstract

The natural product withaferin A (WFA) exhibits antitumor and antiangiogenesis activity in vivo, which results from this drug's potent growth inhibitory activities. Here, we show that WFA binds to the intermediate filament (IF) protein, vimentin, by covalently modifying its cysteine residue, which is present in the highly conserved alpha-helical coiled coil 2B domain. WFA induces vimentin filaments to aggregate in vitro, an activity manifested in vivo as punctate cytoplasmic aggregates that colocalize vimentin and F-actin. WFA's potent dominant-negative effect on F-actin requires vimentin expression and induces apoptosis. Finally, we show that WFA-induced inhibition of capillary growth in a mouse model of corneal neovascularization is compromised in vimentin-deficient mice. These findings identify WFA as a chemical genetic probe of IF functions, and illuminate a potential molecular target for withanolide-based therapeutics for treating angioproliferative and malignant diseases.

Figure 1. Affinity Identification of Binding Target of WFA from Endothelial Cells

(A) Chemical structures of WFA and 12-D WS. (B) Affinity isolation of WFA-B-binding proteins. BAECs were preincubated with DMSO (vehicle) or with 5 μM WFA for 30 min and subsequently with 5 μM WFA-B for 2 hr. Cell lysates prepared in 1% Triton X-100 buffer were purified over NeutrAvidin affinity columns and subjected to SDS-PAGE. The gel was stained with Coomassie blue. The arrow points to the 56 kDa protein band and asterisks mark the coeluted 51 and 43 kDa proteins. (C) WFA-B binds to the 56 kDa protein in HUVECs. Cells were preincubated with DMSO or WFA for 30 min and subsequently with WFA-B for 2 hr. Soluble proteins extracted in 1% Triton X-100 were fractionated by SDS-PAGE and blotted. Blots were developed with Streptavidin-HRP. (D) WFA-B binds vimentin in HUVECs. Cell cultures were preincubated with DMSO (vehicle) or with 5 μM WFA or 1 μM for 30 min and subsequently with 5 μM WFA-B for 2 hr. Cell lysates prepared in 1% Triton X-100 buffer were purified over NeutrAvidin affinity columns and subjected to SDS-PAGE and western blotted with anti-vimentin V9 antibody. The bottom panel represents streptavidin-HRP detection of endogenous biotinylated species used as a loading control. (E) Tetrameric soluble hamster vimentin was incubated with different doses of WFA or inactive congener 12-D WS for 1 hr and subsequently with 0.3 μM WFA-B for 1 hr at 37°C. The proteins were fractionated by SDS-PAGE, blotted and probed with vimentin V9 antibody for loading control, stripped, and reprobed with streptavidin-HRP to detect biotinylated adducts.

Figure 2. WFA Modifies the Unique Cysteine Residue of Vimentin

Tetrameric vimentin was incubated with WFA or DMSO and small molecule-protein complex was subjected to trypsin digestion. The tryptic fragments were subjected to LC-MS/MS analysis. The assignment of fragment ions in the MS/MS of the modified and unmodified peptides were obtained with the SEQUEST software tool “FuzzyIons” (distributed by ThermoFinnigan) to annotate the spectra (A) from WFA-treated sample and (B) from DMSO-treated sample. This analysis verifies both the peptide amino acid sequence and the location and mass of the modification (+470 Daltons on cysteine).

Figure 3. Molecular Model of WFA Binding Site in Tetrameric Vimentin

Molecular modeling of the WFA binding site in the vimentin tetramer model was derived with the crystal structures of the protein fragments associated with the PDB accession code 1gk4. Based on this model, MD-simulated annealing was performed to dock WFA to the vimentin tetramer fragment. The final protein-ligand binding structure was based on MD simulation (with the AMBER 8 program) in a water bath for 1.7 ns. The binding structure is stable in water. Images of the models were generated with PyMol software. (A) Depicted in the figure is a snapshot of the MD-simulated solvent-accessible surface area binding structure showing WFA binding in the cleft between the A and A′ α helices of the vimentin tetramer. (B) The close-up image shows the A-ring twist-boat and B-ring half-chair conformation of WFA [26] (see Figure 1A) is accommodated deep within the binding cleft of the vimentin tetramer, allowing for proper orientation with Cys328 (yellow) to form a covalent bond with the C3 or C6 electrophilic carbon centers of WFA. Note that the exocyclic C27 hydroxyl group (arrow) of WFA to which the linker-biotin was conjugated is orientated toward the solvent-side of the binding cleft that makes it possible for WFA-B to bind tetrameric vimentin. (C) The model shows hydrogen bonding between Gln324 of the vimentin A-helix and the C1 position oxygen atom (2.3 Å), and Asp331 of the vimentin A′ helix and the C4 hydroxyl group (1.7 Å). (D) The alpha orientations of the C5 (OH) and C6-C7 (epoxide) of the inactive withanolide congener 12-D WS appose Cys328 of vimentin, thus preventing nucleophilic attack by the thiol group on the electrophilic carbon centers.

Figure 4. WFA Causes Aggregation of Vimentin Filaments In Vitro and In Vivo

(A) Tetrameric soluble hamster vimentin was polymerized in presence of 170 mM NaCl by incubation at 37°C for 1 hr. The protein was fixed with 0.5% glutaraldehyde, stained with uranyl acetate, and observed by transmission EM. The presence of vehicle solvent does not interfere with filament formation. (B) Polymerization of tetrameric vimentin in the presence of 25 μM WFA produces extensive filamentous aggregates and (C) many irregular fragmented aggregated structures. (D) 12-D WS (25 μM) does not disrupt vimentin polymerization. BAECs treated with DMSO (E, G, I) or 3 μM WFA (F, H, J) for 18 hr were stained for vimentin with a monoclonal anti-vimentin antibody (green) and cos-tained with phalloidin-rhodamine (red). The vimentin (E) and (F) and phalloidin-stained images (G) and (H) in fluorescence overlap reveal the presence of numerous cytoplasmic particulate granules that costain for vimentin and disrupted F-actin in WFA-treated cells compared to controls (I) and (J).

Figure 5. WFA Induces Vimentin Fragmentation in Endothelial Cells

(A) Western blot analysis of HUVECs shows dose-responsive increases in vimentin cleavage products (arrows) with WFA treatment after 2 hr as detected with the monoclonal anti-vimentin V9 antibody. (B) Higher concentrations and longer periods of exposure to WFA (4 hr) cause reduction in levels of the 56 kDa protein (asterisk) and increased abundance of cleavage products of vimentin (arrows). (C) Two-dimensional western blotting analysis of WFA-treated HU-VECs. Cells were extracted with buffer A and soluble lysates were subjected to isoelectric focusing with IPG strips (Biorad). The second dimension was performed with 4%–20% polyacrylamide gels and proteins transferred on membranes for western blot analysis. Protein blots were probed with anti-vimentin monoclonal antibody (V9). IPG strips in the range of pH 4–7 were employed to allow for fine resolution of closely migrating vimentin isoforms. (D–F) Expanded images (range, pH 4–6) of western blots from control (D), WFA- (E), and WFA-B-treated (F) HUVECs show the dramatic reduction in spot intensity of many vimentin isoforms in drug-treated cells.

Figure 6. WFA-Induced Upregulation of Protein Ubiquitination is Mediated by Vimentin

(A) MCF-7 cells that lack endogenous IF proteins were transfected with human vimentin cDNA or a vector control and, after 24 hr, cells were treated with either vehicle or 2 μM WFA for 1 hr. Cell lysates were prepared and equal amounts of protein subjected to SDS-PAGE and protein blots probed with anti-ubiquitin antibody. Blots were reprobed with anti-GAPDH antibody. (B) 20S proteasome (bovine) preparation was incubated with vehicle (control), 0.5 μM, 1.0 μM and 10 μM WFA or with 10 nM Epoxomicin (Epx) in presence of LLVY-AMC substrate at room temperature. Fluorescence readings from triplicate samples were obtained at different time intervals from the 96-well plate with excitation at 355 nm and emission at 430 nm. The release of product was plotted against time for each concentration of inhibitor. (C) Embryonic fibroblast cell lines derived from vimentin-deficient mice and wild-type litter-mates [33] were treated with vehicle, 5 μM WFA, or 5 μM 12-D WS for 24 hr. Cells were harvested and stained with annexin V-FITC and pro-pidium iodide, and extent of apoptosis assessed by flow cytometry. The fold-apoptosis for drug over vehicle-treated samples for each cell line was plotted (n = 2 experiments); error bars represent SD. (D) BAECs were transduced with WFA-modified vimentin and cells were stained after 18 hr. (E) Cells transduced with WFA-modified vimentin show both condensed vimentin filaments localized largely in and around the nucleus and the presence of vimentin-staining particulates. (F and G) Cells transduced with vehicle-treated vimentin show well-distributed orchestration of vimentin IFs (F) and actin cytoskeleton (G). Results representative of three experiments are shown.

Figure 7. Vimentin Mediates the Antiangiogenic Activity of WFA

Wild-type mice and vimentin-deficient mice were subjected to corneal chemical injury with limbal and corneal epithelial cell debridement. Mice were treated by daily intraperiteoneal injection with vehicle, 2 mg/kg WFA, or 2 mg/kg 12-D WS for 10 days. Neovascularization responses in corneas were assessed by flat-mount staining with anti-CD31-flourescent antibodies. (A) Flat-mount stained corneas were photographed and representative images of CD31⁺ (fluorescent) capillaries are shown. (B) Quantification of neovascularization from each group of mice (n = 14, Vim^+/+; n = 10, Vim^−/−) was performed as previously described [45]. Error bars represent SD; * p < 0.05 by Mann-Whitney U test.