IC₅₀ prediction workflow.

<p>Our method is based on two different input streams: (1) cell line features of 77 oncogenes and their mutation state, (2) drug features that are generated with PaDEL software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061318#pone.0061318-Yap1" target="_blank">[19]</a> from the simplified molecular-input line entry system (SMILES), see method section for details. The continuous IC₅₀ value is predicted with state-of-the-art machine learning algorithms (neural networks and random forests).</p

Comparing ANOVA with prediction.

<p>(A) Analysis of variance (ANOVA) of experimental data and predicted output for drug-to-oncogene associations (20% FDR). The size of each association (dot) is proportional to the amount of treated cell lines containing the particular mutated oncogene. Blue dots indicating the same t-test tendency in our predictions, and red ones the opposite. (B) Predicted and measured IC₅₀s of <i>BRAF</i>-mutated vs. wild-type cell lines exposed to the <i>MEK1/2</i>-inhibitor PD-0325901 (p- value of prediction  = 1.91×10⁻⁰⁵, t-test multiple hypothesis corrected with Benjamini & Hochberg).</p

Comparison of single-drug models and the multi-drug model.

<p>The performance of the multi-drug model (red asterisk) and the family of 111 single-drug models (blue histogram) is represented using three different metrics: (A) Pearson correlation R_p, (B) coefficient of determination R², and (C) root mean square error RMSE.</p

IC₅₀ prediction.

<p>Predictions are achieved with 8-fold cross-validations. Performance values are exclusively calculated on the test sets. (A) Correlation between predicted to experimental observed log(IC₅₀) values (Pearson correlation R_p = 0.85 ; coefficient of determination R² = 0.72, root mean square error RMSE  = 0.83). Although there is an enrichment of resistant cell lines, which tend to have higher log(IC₅₀) values than sensitive cell lines, the lower log(IC₅₀) values are still decently predicted. (B) Expected improvement of the IC₅₀ prediction by filling experimentally gaps in the cell-to-drug matrix. The vertical grey line corresponds to the published data set (filled to ∼58%, due to logistic reasons), which corresponds to the results in panel (A). However, similar accuracies (R_p of 0.84 instead of 0.85, R² of 0.70 instead of 0.72) can be achieved using exclusively 20% of the whole matrix.</p

Discovery of a benzo[e]pyrimido-[5,4-b][1,4]diazepin-6(11H)-one as a Potent and Selective Inhibitor of Big MAP Kinase 1

Kinome-wide selectivity profiling of a collection of 2-amino-pyrido[2,3-d]pyrimidines followed by cellular structure−activity relationship-guided optimization resulted in the identification of moderately potent and selective inhibitors of BMK1/ERK5 exemplified by <b>11</b>, <b>18</b>, and <b>21</b>. For example, <b>11</b> possesses a dissociation constant (<i>K</i>_d) for BMK1 of 19 nM, a cellular IC₅₀ for inhibiting epidermal growth factor induced BMK1 autophosphorylation of 0.19 ± 0.04 μM, and an Ambit KINOME<i>scan</i> selectivity score (<i>S</i>₅) of 0.035. Inhibitors <b>18</b> and <b>21</b> are also potent BMK1 inhibitors and possess favorable pharmacokinetic properties which enable their use as pharmacological probes of BMK1-dependent phenomena as well as starting points for further optimization efforts

Discovery of a benzo[e]pyrimido-[5,4-b][1,4]diazepin-6(11H)-one as a Potent and Selective Inhibitor of Big MAP Kinase 1

Kinome-wide selectivity profiling of a collection of 2-amino-pyrido[2,3-d]pyrimidines followed by cellular structure−activity relationship-guided optimization resulted in the identification of moderately potent and selective inhibitors of BMK1/ERK5 exemplified by <b>11</b>, <b>18</b>, and <b>21</b>. For example, <b>11</b> possesses a dissociation constant (<i>K</i>_d) for BMK1 of 19 nM, a cellular IC₅₀ for inhibiting epidermal growth factor induced BMK1 autophosphorylation of 0.19 ± 0.04 μM, and an Ambit KINOME<i>scan</i> selectivity score (<i>S</i>₅) of 0.035. Inhibitors <b>18</b> and <b>21</b> are also potent BMK1 inhibitors and possess favorable pharmacokinetic properties which enable their use as pharmacological probes of BMK1-dependent phenomena as well as starting points for further optimization efforts

Temozolomide enhances PARP inhibitor sensitivity in multiple tumour types.

<p>List of cell lines screened against a combination of olaparib and temozolomide. Whether enhancement of PARP inhibitor sensitivity with temozolomide is observed (✔) or not (✖) is indicated.</p

DNA DSB repair by HR is functional in EWSCs.

<p><b>(A)</b> Western blot of ES8 cells treated with olaparib for the times indicated. Markers are grouped as part of ATM or ATR signaling. Tubulin served as a loading control. (<b>B)</b> Western blot of ES8 cells treated with camptothecin and harvested at various time points following drug washout. GAPDH served as a loading control. <b>(C)</b> Percentage of EdU-positive and EdU-negative ES8 cells with >5 nuclear RAD51 foci following 6-hour treatment with vehicle or olaparib (ola). <b>(D)</b> Olaparib log GI₅₀ (μM) of cell lines mock-transfected or transfected with CtIP or BRCA1 siRNA as indicated.</p

EWSCs are sensitive to PARP inhibition and S-phase DNA-damaging agents.

<p><b>(A)</b> and <b>(C)</b> Scatter plots of IC₅₀ (μM) values on a log scale comparing drug sensitivity of <i>EWS-FLI1</i>-positive and wild-type (WT) <i>EWS-FLI1</i>-negative cell lines to (A) four PARPi and (C) camptothecin and cisplatin. The sample size (n) is indicated and each circle represents the IC₅₀ of one cell line. The red bar is the geometric mean and the drug name is depicted above each plot along with the significance of the association as determined by an unpaired two-sample t-test. <b>(B)</b> Long term viability assays in EWSCs were performed in the presence of vehicle (-) or increasing concentrations of four PARPi as indicated. Non-EWSC lines (U-2-OS and HeLaSF) are included for comparison. These data are representative of 3 independent experiments.</p

EWSCs are sensitive to PARP1 trapping.

<p><b>(A)</b> Relative viability of mock-transfected and PARP1 siRNA-transfected ES8 cells treated with vehicle or olaparib. Asterisks indicate <i>student’s paired t-test P</i> value **P<0.01, ns = not significant. <b>(B)</b> PARP1 expression in cells transfected with a scrambled control or a titration of PARP1_1 siRNA and their relative viability following treatment with vehicle or olaparib. <b>(C)</b> IC50 values of parental ES8 and PARPi-resistant OLAR5 cells to five different PARPi and the fold difference between them. <b>(D)</b> Western blot of PARP1 expression in ES8 and OLAR5 cells. Viability values are the mean of technical triplicates and representative of 3 independent experiments.</p