Chemical Probes that Competitively and Selectively Inhibit Stat3 Activation

Signal transducer and activator of transcription (Stat) 3 is an oncogene constitutively activated in many cancer systems where it contributes to carcinogenesis. To develop chemical probes that selectively target Stat3, we virtually screened 920,000 small drug-like compounds by docking each into the peptide-binding pocket of the Stat3 SH2 domain, which consists of three sites—the pY-residue binding site, the +3 residue-binding site and a hydrophobic binding site, which served as a selectivity filter. Three compounds satisfied criteria of interaction analysis, competitively inhibited recombinant Stat3 binding to its immobilized pY-peptide ligand and inhibited IL-6-mediated tyrosine phosphorylation of Stat3. These compounds were used in a similarity screen of 2.47 million compounds, which identified 3 more compounds with similar activities. Examination of the 6 active compounds for the ability to inhibit IFN-γ-mediated Stat1 phosphorylation revealed that 5 of 6 were selective for Stat3. Molecular modeling of the SH2 domains of Stat3 and Stat1 bound to compound revealed that compound interaction with the hydrophobic binding site was the basis for selectivity. All 5 selective compounds inhibited nuclear-to-cytoplasmic translocation of Stat3, while 3 of 5 compounds induced apoptosis preferentially of breast cancer cell lines with constitutive Stat3 activation. Thus, virtual ligand screening of compound libraries that targeted the Stat3 pY-peptide binding pocket identified for the first time 3 lead compounds that competitively inhibited Stat3 binding to its pY-peptide ligand; these compounds were selective for Stat3 vs. Stat1 and induced apoptosis preferentially of breast cancer cells lines with constitutively activated Stat3

Summary of activity of compounds in inhibiting Stat3 binding to pY peptide ligand in a surface plasmon resonance binding (SPR) assay, in inhibiting IL-6-mediated Stat3 phosphorylation (pStat3) and in inhibiting IL-6-mediated Stat3 nuclear translocation in a high-throughput fluorescence microscopy (HTFM) assay.

1<p>Data presented are IC₅₀ values (µM) obtained using results summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#pone-0004783-g001" target="_blank">Figures 1 (SPR)</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#pone-0004783-g002" target="_blank">Figure 2 (pStat3)</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#pone-0004783-g004" target="_blank">Figure 4 (HTFM)</a>.</p

Summary of compound chemical names and formulas.

1<p>Compound name given by our lab.</p

Computer modeling of each compound bound by the SH2 domain of Stat3 or Stat1.

<p>The 2-D structures and the results of computer docking of each compound to the Stat3 SH2 domain are shown in panels A through F. The left side of each panel shows the 2-D structure, the middle portion of each panel shows the compound binding to an electrostatic molecular surface model of the Stat3 SH2 domain in which blue represents areas of positive-charge and red represents areas of negative-charge. The right side of each panel is a closer view of this interaction with hydrogen bonds indicated by dotted lines. Stick models are used to depict critical residues in the general binding site (R609, K591, S611, E612 and S613), in the specific binding site (E638) and in the hydrophobic site (W623, Q635, V637, Y640 and Y657) with carbon, oxygen, nitrogen and hydrogen atoms represented by silver, red, blue and grey, respectively. Each compound is depicted using a ball-and-stick model with carbon, oxygen, nitrogen, sulfur, chlorine and hydrogen atoms represented by gold, red, blue, yellow and green, respectively. In panel A, the negatively charged benzoic acid moiety of Cpd3 has electrostatic interactions with the guanidinium cation group of R609 and the basic ammonium group of K591. There are double H-bonds that form between the carboxylic oxygen and the side chain terminus hydrogen of R609 and the amide hydrogen of E612 and H-bond formation between the benzoic acid carbonyl oxygen and the side chain hydroxyl hydrogen of S611. The oxygen atom of 1,4-benzodioxin forms a hydrogen bond with the amide hydrogen of E638. In addition, the double ring group of Cpd3 has hydrophobic interactions to the hydrophobic binding site, which consists of W623, Q635, V637, Y640, and Y657. In panel B, the carboxylic terminus of the benzoic acid moiety of Cpd30 has electrostatic interactions with the to guanidinium group of R609. There are two hydrogen bonds that form between the terminal hydrogen of R609 and carboxylic oxygen of Cpd30 and between the terminal hydrogen of S613 and carbonyl oxygen of Cpd30. In addition, the thiazolidin moiety of Cpd30 has hydrophobic interactions with the hydrophobic binding site. In panel C, the (carboxymethyl) thio moiety of Cpd188 has electrostatic interactions with R609 and K591. The terminal oxygen of the (carboxymethyl) thio group of Cpd188 forms three H-bonds: 1) with the guanidinium hydrogen of R609, 2) with the backbone amide hydrogen of E612 and 3) with the hydroxyl-hydrogen of S611. There is an H-bond formation between the hydroxyl-oxygen of the benzoic acid group of Cpd188 and the amide-hydrogen of E638. In addition, the benzoic acid group interacts with the hydrophobic binding site, particularly V637. In panel D, the benzoic acid group of Cpd3-2 has electrostatic interactions with R609 and K591. There are two H bonds between the carboxylic oxygen of the benzoic acid group and guanidinium hydrogen of R609 and between the carbonyl oxygen of the benzoic acid group and the hydroxyl hydrogen of S611. In addition, the 1,3-dihydro-2H-inden-2-ylidene group of Cpd30 has hydrophobic interactions with the hydrophobic binding site. In panel E, H-bond formation occurs between the carbonyl-oxygen of the benzoate moiety at the double-ring end of Cpd3-7 and the side chain hydroxyl hydrogen of S611 and the amide hydrogen of S613. H-bond formation also occurs the between the hydroxyl oxygen of Cpd3-7 and the guanidinium hydrogen of R609 and a hydrogen within the ammonium terminus of K591. In addition, the single ring group of Cpd3-7 has hydrophobic interactions with the hydrophobic binding site. In panel F, there are electrostatic interactions between the benzoic acid group of Cpd30-12 and R609 and K591. H-bond formation occurs between the carbonyl-oxygen of Cpd30-12 and the guanidinium-hydrogen of R609, between the carboxyl-oxygen of Cpd30-12 and the hydroxyl-hydrogen of S611 and between the furyl oxygen of Cpd30-12 and hydrogen within the ammonium terminus of K591. Panel G shows the sequence alignment of residues 585 to 688 of Stat3 and residues 578 to 682 of Stat1 each containing their respective SH2 domains. Residues K591, R609, S611, E612 and S613 that bind the pY residue are indicated in blue. Residue E638 that binds to the +3 residue is indicated in green. Residues W623, Q635, V637, Y640 and Y657 comprising the hydrophobic binding site are indicated in orange; the region within Stat3 and Stat1 that contains the hydrophobic binding site is boxed. Residues within Loop_βC–βD and Loop_αC–αD of Stat3 are each underlined. Residues identical between Stat3 and Stat1 are indicated by a dot. Panel H shows an overlay of tube-and-ribbon models of the SH2 domains of Stat3 (green) and Stat1 (gray). Residues within the hydrophobic binding surface of each are shown as stick models and Loop_βC–βD and Loop_αB–αC are indicated. The van der Waals energy of each compound bound to the Stat1 SH2 domain or the Stat3 SH2 domain was calculated, normalized to the value for Stat1 and shown in panel I.</p

Inhibition of Stat3 binding to immobilized phosphopeptide ligand by compounds.

<p>Binding of recombinant Stat3 (500 nM) to a BiaCore sensor chip coated with a phosphododecapeptide based on the amino acid sequence surrounding Y1068 within the EGFR was measured in real time by SPR in the absence (0 µM) or presence of increasing concentrations (0.1 to 1,000 µM) of Cpd3 (panel A), Cpd30 (panel B), Cpd188 (panel C), Cpd3-2 (panel D), Cpd3-7 (panel E) and Cpd30-12 (panel F). Data shown are response units as a function of time in seconds and are representative of 2 or more experiments. The equilibrium binding levels obtained in the absence or presence of compound were normalized (response obtained in the presence of compound ÷ the response obtained in the absence of compound ×100) and plotted against the log concentration (nM) of the compound (panel G). The experimental points for each compound fit to a competitive binding curve that uses a four-parameter logistic equation (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#s2" target="_blank">Methods</a> for details). These curves were used to calculate the IC₅₀ value for each compound (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#pone-0004783-t002" target="_blank">Table 2</a>).</p

Effect of compounds on ligand-mediated Stat3 and Stat1 phosphorylation.

<p>HepG2 cells were pretreated with DMSO alone or DMSO containing Cpd3 (panel A), Cpd188 (panel B), Cpd30 (panel C), Cpd3-2 (panel D), Cpd3-7 (panel E) or Cpd30-12 (panel F) at the indicated concentration for 60 min. Cells were then stimulated with IL-6 (30 ng/ml) for 30 min. Protein extracts of cells were separated by SDS-PAGE, blotted and developed serially with antibodies to pStat3, total Stat3 and β-actin. Blots were stripped between each antibody probing. Band intensities were quantified by densitometry. The value of each pStat3 band was divided by its corresponding total Stat3 band intensity; the results were normalized to the DMSO-treated control value. This value was plotted as a function of the log compound concentration. The best-fitting curve was determined using 4-Parameter Logistic Model/Dose Response/XLfit 4.2, IDBS software and was used to calculate the IC₅₀ value (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#pone-0004783-t001" target="_blank">Table 1</a>). Each panel is representative of 3 or more experiments. In panel G, HepG2 cells were pretreated with DMSO alone or DMSO containing each of the compounds at a concentration of 300 µM for 60 min. Cells were then stimulated with IFN-γ (30 ng/ml) for 30 min. Protein extracts of cells were separated by SDS-PAGE and immunoblotted serially with antibodies to pStat1, total Stat1 and β-actin. Blots were stripped between each immunoblotting. The results shown are representative of 2 or more experiments.</p

Summary of activity of compounds that are selective for Stat3 in inducing apoptosis of breast cancer cell lines.

1<p>CAM, camptothecin.</p>2<p>Data presented are EC₅₀ values (µM) calculated from results summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004783#pone-0004783-g005" target="_blank">Figure 5</a>.</p