1. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 1/18 Docking@Grid validation Docking@Grid ANR meeting - 28/10/2008 CEA Grenoble - DSV/iRTSV/CMBA (C. Barette, L. Lafanechère) et LTS (R. Prudent, C. Cochet) Laboratoire dinfochimie, ULP, Strasbourg (S. Conilleau, D. Horvath) LIFL, Lille (team of E.-G. Talbi) L. Brillet, S. Roy (CEA Grenoble - DSV/iRTSV/CMBA)

2. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 2/18 Introduction folding redocking of PDB complexes comparison with classical docking programs activity prediction DOCKING@GRID EVALUATION 1. Preparation of the PDB complexes 2. Evaluation with the protein kinase CK2 – comparison with Gold

3. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 3/18 Thrombin CK2 HIV-RT 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 PREPARATION OF THE COMPLEXES 3 families of PDB complexes redocking : 3BQC.pdb (human) 23 ligands (human + maize) 1RT1.pdb 11 ligands 1XM1.pdb 10 ligands Tools : Chimera, MOE, VegaZZ, ChemAxon

4. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 4/18 Evaluation with the protein kinase CK2 ATP or GTP Protein – substrate phosphate + 300 substrates CK2 abnormal expression: inflammation (viral) infection cancer PROTEIN KINASE CK2

5. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 5/18 in vitro activity in vivo activity selectivity SAR Database JChemBase (ChemAxon) CK2 BIOLOGICAL DATA 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 Evaluation with the protein kinase CK2 CEA Grenoble, DSV/iRTSV/CMBA: C. Barette, L. Lafanechère HTS screening: ~ 12 000 compounds post HTS studies: 5 groups of actives / inactives structural analogues (~ 100 compounds)

6. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 6/18 EVALUATION WITH CK2 – COMPARISON DOCKING@GRID - GOLD EVALUATION WITH CK2 – COMPARISON DOCKING@GRID - GOLD Docking@Grid Gold (CCDC) co-cristallised ligands set of analogues (known activity) CMBA library (CEA): 35000 comp. co-cristallised ligands others ? docking results Comparison ? 1 protein conformation Hits selection in vitro tests

7. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 7/18 GoldGlideFlexX PRELIMINARY STUDIES Comparison Docking@Grid - Gold Revue of the litterature (docking, evaluation of the docking programs) Training in D. Rognans laboratory (Strasbourg) Choice of a docking program

8. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 8/18 1.Bibliography 2.Preparation of the target 3.Preparation of the library 4.Design of the screening parameters 5.Screening of the library 6.Post-processing / results analysis VIRTUAL SCREENING ON CK2 WITH GOLD Developed strategy: Comparison Docking@Grid - Gold

9. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 9/18 33 publications 25 cristallised inhibitors-CK2 complexes (PDB) - structure - flexibility - water molecules ? - binding modes / interactions BIBLIOGRAPHY Comparison Docking@Grid - Gold information about the active site:

10. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 10/18 emodin, 3BQC.pdb Lys68 green = hydrophobic pink = polar

11. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 11/18 PREPARATION OF THE TARGET Comparison Docking@Grid - Gold Preparation Choice of the conformation

12. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 12/18 Unique ID Protonation pH 7.4 Tautomers Standardisation 2D 3D PREPARATION OF THE LIBRARY x x x x x Comparison Docking@Grid - Gold automated procedure:

13. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 13/18 DESIGN OF THE SCREENING PARAMETERS 1 - Docking of PDB complexes check the pose (RMSD < 2A ?) Comparison Docking@Grid - Gold 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 failures : no flexibility of the hinge region good success rate

14. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 14/18 2 - Docking of a small set of actives / inactives check the enrichment in actives actives inactives % of actives % of compounds ranked by score 100% random enrichment Comparison Docking@Grid - Gold DESIGN OF THE SCREENING PARAMETERS

15. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 15/18 POST-PROCESSING / RANKING OF THE MOLECULES Strategies: based on interaction fingerprints + diversity analysis Comparison Docking@Grid - Gold based on a consensus of scoring functions Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints, G. Marcou & D. Rognan, 2007, J. Chem. Inf. Model.

16. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 16/18 EVALUATION WITH CK2 – COMPARISON DOCKING@GRID - GOLD EVALUATION WITH CK2 – COMPARISON DOCKING@GRID - GOLD Docking@Grid Gold (CCDC) co-cristallised ligands set of analogues (known activity) CMBA library (CEA): 35000 comp. co-cristallised ligands others ? docking results Comparison ? 1 protein conformation Hits selection in vitro tests

17. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 17/18 CEA: CMBA (C. Barette, L. Lafanechère), LTS (R. Prudent, C. Cochet, V. Moucadel), Laboratoire dInfochimie (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 dInformatique Fondamentale de Lille: team of E.-G. Talbi Conclusion THANKS

18. L. Brillet (CEA) – Docking@Grid ANR meeting – META08 Hammamet 18/18 Docking@Grid validation Docking@Grid ANR meeting - 28/10/2008 CEA Grenoble - DSV/iRTSV/CMBA (C. Barette, L. Lafanechère) et LTS (R. Prudent, C. Cochet) Laboratoire dinfochimie, ULP, Strasbourg (D. Horvath, S. Conilleau) LIFL, Lille (team of E.-G. Talbi) L. Brillet, S. Roy (CEA Grenoble - DSV/iRTSV/CMBA)