1. www.hp-see.eu HP-SEE In the search of the HDAC-1 inhibitors. The preliminary results of ligand based virtual screening Ilija N. Cvijetić, Ivan O. Juranić, Alessandro Pedretti, Giulio Vistoli, Branko J. Drakulić ilija@chem.bg.ac.rs The HP-SEE initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no. 261499

2. Methodology - Shape and electrostatics play crucial role in ligand-receptor interactions - ROCS compares the molecules by the shape and pharmacophoric similarity - EON compares molecules by electrostatic similarity HP-SEE User Meeting – Belgrade 19-10-20122 * http://www.eyesopen.comhttp://www.eyesopen.com - The OpenEye* applications are fully functional on our home cluster PARADOX - Part of the source codes were made for the ligand-based virtual screening - Installed applications are industry standards - OMEGA generate conformers

3. Virtual Screening HP-SEE User Meeting – Belgrade 19-10-20123 - Majority of those compounds are available - Potentially, any can act on some of biological targets - One of the methods for the selection of compounds that could act on chosen target is virtual screening - Significantly faster and cheaper, comparing to biological tests - At the end of this year 70 th million small molecule should be added to Chemical abstract database * http://web.cas.org/forms/70million.htmlhttp://web.cas.org/forms/70million.html

4. Virtual Screening HP-SEE User Meeting – Belgrade 19-10-20124 - Ligand based – significantly faster - Structure based – known structure of the receptor - Why structurally dissimilar compounds act on same receptors?

5. Virtual Screening HP-SEE User Meeting – Belgrade 19-10-20125

6. Background HP-SEE User Meeting – Belgrade 19-10-20126 - Inhibition of histone deacetylases (HDACs) elicits anticancer effects in several tumor cells by inhibition of cell growth and inducing cell differentiation - Acetylation and deacetylation of proteins are important regulatory mechanisms of cellular events - Histone deacetylases (HDACs) are involved in acetylation of lysine residues of histone and non-histone proteins

7. Background HP-SEE User Meeting – Belgrade 19-10-20127 - Classification of histone deacetylases: Class I - HDAC1,HDAC2, HDAC3, and HDAC8 - Class I and II HDACs are overexpressed in ovarian (HDAC 1- 3), lung (HDAC 1 and 3) and gastric cancer (HDAC2); Class I and II HDAC inhibitors have been approved as anti- cancer therapeutics Class II - HDAC4, HDAC5, HDAC6, HDAC7, HDAC9, HDAC10 Class IV – HDAC 11 Class III is a series of the NAD + -dependent Sir2 family of enzymes - Class I and II and IV HDACs are Zn 2+ - containing hydrolases; class III are NAD + dependent

8. Binding site HP-SEE User Meeting – Belgrade 19-10-20128 HDAC 2 PDB code: 3MAX

9. Binding site HP-SEE User Meeting – Belgrade 19-10-20129 Hydrophobic Hydrophilic

10. Binding site HP-SEE User Meeting – Belgrade 19-10-201210 Hydrophobic Hydrophilic

11. Template and database HP-SEE User Meeting – Belgrade 19-10-201211 - Ligand from the PDB entry 3MAX - Database: ChemBank – comprise 2346 molecules - After the filtering 1990 molecules - Significantly larger databases available – up to few million of compounds

12. Results HP-SEE User Meeting – Belgrade 19-10-201212 - 1990 molecules from database were submitted to OMEGA ~ 142000 conformations were generated -Pharmacophoric and shape similarity was searched with the ROCS program - 100 hits were selected according to the Tanimoto index - For the objects A and B, Tanimoto index represents the ratio of common elements and the all elements in both objects - Multiconformer set was compared against the template

13. Results – 13 HP-SEE User Meeting – Belgrade 19-10-201213 Shape Tanimoto score Color Tanimoto score Tanimoto Combo score - Color force field – Implicit MillsDean and Explicit MillsDean - Color force-fields include 6 pharmacophoric features: - Implicit MillsDean – includes protonation state at pH = 7 Hydrogen-bond donors, hydrogen-bond acceptors, hydrophobes, anions, cations, and rings Scoring

14. Results – 14 HP-SEE User Meeting – Belgrade 19-10-201214 Color force field of the template ligand

15. Results – 15 HP-SEE User Meeting – Belgrade 19-10-201215 - The best ranked molecule from the ROCS search was Nifenazone – TanimotoCombo Score 1.305 - It has been used as the analgesic drug. - Withdrawn due to heavy side effects 2D structure of Nifenazone

16. Results – 16 HP-SEE User Meeting – Belgrade 19-10-201216 - Electrostatic similarity study of the ROCS output (best ranked conformation per molecule) against the template molecule was performed in EON program - The 100 top ranked molecules from ROCS output was used - Electrostatic grids of the molecules were compared - Tanimoto index as a scoring function - The best scored was itdac-7, Tanimoto score 1.403 - MMFF94s charges were used - The itdac7 was proved as the modulator of Sir2 deacetylase

17. Results – 17 HP-SEE User Meeting – Belgrade 19-10-201217 Electrostatic comparison of the template (green) and the itdac-7 (gray)

18. Performance and further objectives – 18 HP-SEE User Meeting – Belgrade 19-10-201218 Screening of the much larger databases: - ZINC (over 21 milion compounds), http://zinc.docking.org/ http://zinc.docking.org/ - Commercial Compound Collection (CoCoCo), 7 milion compounds, http://cococo.unibo.it/ http://cococo.unibo.it/ - Assigning more reliable charges to the ROCS hits - Validation of hits obtained - 5.1 molecules/sec in average - 400 overlays/sec - 16 cpu, OpenEye MPI Performance Further objectives - executed with pbs

19. Conclusions - All Openeye applications installed on our home cluster are fully functional - We obtained the hit molecule that have been approved as the modulator of enzymes involved in deacetylations - Can run on several nodes - OpenMPI via pbs - Good scalability for reported calculations HP-SEE User Meeting – Belgrade 19-10-201219

20. Conclusion Thank you for your attention! – 20 HP-SEE User Meeting – Belgrade 19-10-201220