Docking@Grid validation

1. Docking@Grid ANR meeting - 28/10/2008 Docking@Grid validation L. Brillet, S. Roy (CEA Grenoble - DSV/iRTSV/CMBA) • CEA Grenoble - DSV/iRTSV/CMBA (C. Barette, L. Lafanechère) et LTS (R. Prudent, C. Cochet) • Laboratoire d’infochimie, ULP, Strasbourg (S. Conilleau , D. Horvath) • LIFL, Lille (team of E.-G. Talbi)

2. Introduction DOCKING@GRID EVALUATION • folding • redocking of PDB complexes • comparison with classical docking programs • activity prediction 1. Preparation of the PDB complexes 2. Evaluation with the protein kinase CK2 – comparison with Gold

3. PREPARATION OF THE COMPLEXES 3 families of PDB complexes  redocking : CK2 HIV-RT Thrombin 3BQC.pdb (human) 23 ligands (human + maize) 1RT1.pdb 11 ligands 1XM1.pdb 10 ligands • reference coordinates for ligands  superimposition of the complexes’ structures • preparation of the target H, charges, atomic types, file format, active site • preparation of the ligands  corrections, H, charges, atomic types, file format Tools : Chimera, MOE, VegaZZ, ChemAxon

4. Evaluation with the protein kinase CK2 Protein – substrate ATP or GTP PROTEIN KINASE CK2 phosphate + 300 substrates CK2 abnormal expression: • inflammation • (viral) infection • cancer

5. Evaluation with the protein kinase CK2 CK2 BIOLOGICAL DATA CEA Grenoble, DSV/iRTSV/CMBA: C. Barette, L. Lafanechère • in vitro activity • in vivo activity • selectivity • SAR CEA Grenoble, DSV/iRTSV/LTS: R. Prudent, C. Cochet • Expanding the chemical diversity of CK2 inhibitors, Prudent et al., 2008, Mol. Cell. Biochem. • Salicylaldehyde derivatives as new protein kinase CK2 inhibitors, Prudent et al., 2008, Bioch. Biophys. Acta • HTS screening: ~ 12 000 compounds • post HTS studies: 5 groups of actives / inactives structural analogues (~ 100 compounds) Database JChemBase (ChemAxon)

6. EVALUATION WITH CK2 – COMPARISON DOCKING@GRID - GOLD Docking@Grid Gold (CCDC)  1 protein conformation • co-cristallised ligands • set of analogues (known activity) • CMBA library (CEA): 35000 comp. • co-cristallised ligands • others ? docking docking Comparison ? results results Hits selection  in vitro tests

7. Comparison Docking@Grid - Gold PRELIMINARY STUDIES • Revue of the litterature (docking, evaluation of the docking programs) • Training in D. Rognan’s laboratory (Strasbourg) • Choice of a docking program Gold Glide FlexX

8. Comparison Docking@Grid - Gold VIRTUAL SCREENING ON CK2 WITH GOLD • Bibliography • Preparation of the target • Preparation of the library • Design of the screening parameters • Screening of the library • Post-processing / results analysis Developed strategy:

9. Comparison Docking@Grid - Gold BIBLIOGRAPHY • 33 publications • 25 cristallised inhibitors-CK2 complexes (PDB) • information about the active site: - structure - flexibility - water molecules ? - binding modes / interactions

10. Lys68 green = hydrophobic pink = polar emodin, 3BQC.pdb

11. Comparison Docking@Grid - Gold PREPARATION OF THE TARGET • Choice of the conformation • Preparation

12. Comparison Docking@Grid - Gold PREPARATION OF THE LIBRARY automated procedure: • Unique ID • Protonation pH 7.4 • Tautomers • Standardisation • 2D  3D x x x x x

13. Comparison Docking@Grid - Gold DESIGN OF THE SCREENING PARAMETERS 1 - Docking of PDB complexes check the pose (RMSD < 2A ?) • Docking protocole variations with Gold : • water molecule n°2 • flexibility of the lateral chains • number of genetic operations for each genetic algorithm run • number of genetic algorithm runs per ligand good success rate failures : no flexibility of the hinge region

14. Comparison Docking@Grid - Gold DESIGN OF THE SCREENING PARAMETERS 2 - Docking of a small set of actives / inactives check the enrichment in actives % of actives enrichment 100% actives random inactives 100% % of compounds ranked by score

15. Comparison Docking@Grid - Gold POST-PROCESSING / RANKING OF THE MOLECULES Strategies: • based on interaction fingerprints Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints, G. Marcou & D. Rognan, 2007, J. Chem. Inf. Model. • based on a consensus of scoring functions + diversity analysis

16. EVALUATION WITH CK2 – COMPARISON DOCKING@GRID - GOLD Docking@Grid Gold (CCDC)  1 protein conformation • co-cristallised ligands • set of analogues (known activity) • CMBA library (CEA): 35000 comp. • co-cristallised ligands • others ? docking docking Comparison ? results results Hits selection  in vitro tests

17. Conclusion THANKS • CEA: CMBA (C. Barette, L. Lafanechère), LTS (R. Prudent, C. Cochet, V. Moucadel), • Laboratoire d’Infochimie (ULP, Strasbourg): S. Conilleau, D. Horvath, G. Marcou • Bioinformatique du Médicament, Laboratoire de Pharmacochimie et de la Communication Cellulaire (ULP, Illkirch): D. Rognan and his team • CEA: GIPSE (C. Charavay, V. Dorffer, J.-P. Eynar), IBS (A. Thomas) • M. Lopez-Ramos (Institut Curie, Paris), J.-N. Denis (UJF), D. Giganti (Institut Pasteur, Paris) • Laboratoire d’Informatique Fondamentale de Lille: team of E.-G. Talbi

18. Docking@Grid ANR meeting - 28/10/2008 Docking@Grid validation L. Brillet, S. Roy (CEA Grenoble - DSV/iRTSV/CMBA) • CEA Grenoble - DSV/iRTSV/CMBA (C. Barette, L. Lafanechère) et LTS (R. Prudent, C. Cochet) • Laboratoire d’infochimie, ULP, Strasbourg (D. Horvath, S. Conilleau) • LIFL, Lille (team of E.-G. Talbi)