Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization

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Analysis of Iterative Screening with Stepwise Compound Selection Based on Novartis In-house HTS Data.

With increased automation and larger compound collections, the development of high-throughput screening (HTS) started replacing previous approaches in drug discovery from around the 1980s onward. However, even today it is not always appropriate, or even feasible, to screen large collections of compounds in a particular assay. Here, we present an efficient method for iterative screening of small subsets of compound libraries. With this method, the retrieval of active compounds is optimized using their structural information and biological activity fingerprints. We validated this approach retrospectively on 34 Novartis in-house HTS assays covering a wide range of assay biology, including cell proliferation, antibacterial activity, gene expression, and phosphorylation. This method was employed to retrieve subsets of compounds for screening, where selected hits from any given round of screening were used as starting points to select chemically and biologically similar compounds for the next iteration. By only screening ∼1% of the full screening collection (∼15 000 compounds), the method consistently retrieves diverse compounds belonging to the top 0.5% of the most active compounds for the HTS campaign. For most of the assays, over half of the compounds selected by the method were found to be among the 5% most active compounds of the corresponding full-deck HTS. In addition, the stringency of the iterative method can be modified depending on the number of compounds one can afford to screen, making it a flexible tool to discover active compounds efficiently.S. Paricharak thanks the Netherlands Organisation for Scientific Research (NWO, grant number NWO-017.009-065), Novartis Institutes for BioMedical Research (NIBR) and the Prins Bernhard Cultuurfonds for funding and C. Parker, M. Frederiksen, G. Landrum and N. Fechner for insightful discussions.This is the author accepted manuscript. The final version is available from ACS Publications via http://dx.doi.org/10.1021/acschembio.6b0002

Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-gamma

Hepatocellular carcinoma, a fatal liver cancer, affects 600 000 people annually and ranks third in cancer-related lethality. In this work we report the synthesis and related biological activity of novel dihydropyrimidones. Among the tested compounds, 5-acetyl-4-(1H-indol- 3-yl)-6-methyl-3,4-dihydropyrimidin-2(1H)-one (4g) was found to be most active towards the HepG2 cell line (IC50 = 17.9 mu M), being at the same time 7.6-fold selective over normal (LO2) liver cells (IC50 = 136.9 mu M). Subsequently, we identified peroxisome proliferator-activated receptor gamma as a target of compound 4g using an in silico approach, and confirmed this mode-of-action experimentally

Trisubstituted-imidazoles induce apoptosis in human breast cancer cells by targeting the oncogenic PI3K/Akt/mTOR signaling pathway

Overactivation of PI3K/Akt/mTOR is linked with carcinogenesis and serves a potential molecular therapeutic target in treatment of various cancers. Herein, we report the synthesis of trisubstituted-imidazoles and identified 2-chloro-3-(4, 5-diphenyl-1H-imidazol-2-yl) pyridine (CIP) as lead cytotoxic agent. Naïve Base classifier model of in silico target prediction revealed that CIP targets RAC-beta serine/threonine-protein kinase which comprises the Akt. Furthermore, CIP downregulated the phosphorylation of Akt, PDK and mTOR proteins and decreased expression of cyclin D1, Bcl-2, survivin, VEGF, procaspase-3 and increased cleavage of PARP. In addition, CIP significantly downregulated the CXCL12 induced motility of breast cancer cells and molecular docking calculations revealed that all compounds bind to Akt2 kinase with high docking scores compared to the library of previously reported Akt2 inhibitors. In summary, we report the synthesis and biological evaluation of imidazoles that induce apoptosis in breast cancer cells by negatively regulating PI3K/Akt/mTOR signaling pathway

Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules

International audienceThe rampant increase of public bioactivity databases has fostered the development of computational chemogenomics methodologies to evaluate potential ligand-target interactions (polypharmacology) both in a qualitative and quantitative way. Bayesian target prediction algorithms predict the probability of an interaction between a compound and a panel of targets, thus assessing compound polypharmacology qualitatively, whereas structure-activity relationship techniques are able to provide quantitative bioactivity predictions. We propose an integrated drug discovery pipeline combining in silico target prediction and proteochemometric modelling (PCM) for the respective prediction of compound polypharmacology and potency/affinity. The proposed pipeline was evaluated on the retrospective discovery of Plasmodium falciparum DHFR inhibitors. The qualitative in silico target prediction model comprised 553,084 ligand-target associations (a total of 262,174 compounds), covering 3,481 protein targets and used protein domain annotations to extrapolate predictions across species. The prediction of bioactivities for plasmodial DHFR led to a recall value of 79% and a precision of 100%, where the latter high value arises from the structural similarity of plasmodial DHFR inhibitors and T. gondii DHFR inhibitors in the training set. Quantitative PCM models were then trained on a dataset comprising 20 eukaryotic, protozoan and bacterial DHFR sequences, and 1,505 distinct compounds (in total 3,099 data points). The most predictive PCM model exhibited R 2 0 test and RMSE test values of 0.79 and 0.59 pIC 50 units respectively, which was shown to outperform models based exclusively on compound (R 2 0 test /RMSE test = 0.63/0.78) and target information (R 2 0 test /RMSE test = 0.09/1.22), as well as inductive transfer knowledge between targets, with respective R 2 0 test and RMSE test values of 0.76 and 0.63 pIC 50 units. Finally, both methods were integrated to predict the protein targets and the potency on plasmodial DHFR for the GSK TCAMS dataset, which comprises 13,533 compounds displaying strong anti-malarial activity. 534 of those compounds were identified as DHFR inhibitors by the target prediction algorithm, while the PCM algorithm identified 25 compounds, and 23 compounds (predicted pIC 50 > 7) were identified by both methods. Overall, this integrated approach simultaneously provides target and potency/affinity predictions for small molecules

Electrocatalytical properties of Au(111-25nm) - Pd quasi-single crystal film electrodes as probed by ATR-SEIRAS

Electrochemical and electrocatalytic properties of thin films Au(111-25 nm), which are quasi-single-crystal electrodes 25 nm thick made of gold with the (I 11) preferential orientation, and same electrodes modified with a monolayer (ML) of palladium are studied in 0.1 M solutions of HClO4 and H2SO4 employing voltammetric techniques and surface enhanced infrared reflection absorption spectroscopy (ATR-SEIRAS). Spectroscopic experiments demonstrate strong adsorption of electrolyte species (H2O, OHads, anions) on the Pd surface. The weak and reversible adsorption of CO on Au(111-25 nm) does not change the interfacial-water structure. Adsorption of CO on the Pd-modified film results in an irreversibly adsorbed CO adlayer stabilized by co-adsorbed isolated water species. Various electrooxidation mechanisms are discussed. Electrochemical and spectroscopic investigations on the adsorption and electrooxidation of HCOOH on bare and I ML Pd-Au(111-25 nm) electrodes reveal that electrooxidation proceeds in both cases via a direct or dehydrogenation pathway. This mechanism involves the formation of formate as intermediate, which is detected by in situ ATR-SEIRAS. The reactivity on Pd-modified surfaces is higher than on bare gold. The specifically adsorbed anions (sulfate/bisulfate) and the oxide formation on the substrate surface lower the reactivity for CO and HCOOH on both surfaces