1. Fast Computational Method for Fragment Growing and Joining Using Molecular Fields Dr Martin J Slater

2. Cresset BMD: Who are we? > Cresset was founded in 2002 by innovator Andy Vinter > We provide and continually develop a suite of unique cutting edge molecular modelling software for drug discovery. > We have clients from big pharma, agrochem, biotech and academia

3. Cresset’s unique technology > It uses a condensed 3D representation of the electrostatic, hydrophobic and shape properties of molecules together with the full fields. 3D Molecular Electrostatic Potential (MEP) What proteins see? Field Points 2D Representation What chemists see? = Positive = Negative = Shape = Hydrophobic What our CPUs see?

4. > Field patterns from Cresset’s proprietary XED force field reproduce experimental results XEDs make fields work Interaction of Acetone and Any-OH from small molecule crystal structures ExperimentalUsing XEDsNot using XEDs XED adds p-orbitals to get better representation of atoms

5. Biologically Relevant Molecular Comparisons Bioisosteres Bioisosteric groups

6. View fields Field points give you new insights into your molecule Experimental (Data from small molecule xray structures) Fields Structure

7. Comparing 2D and 3D metrics Similar 2D=3D_FS 2D=3D Dissimilar 2D=3D_FS 2D = 3D_FS

8. Example - Higher 3D Sim 2D sim = 0.1 (other methods=0.3) 3D field sim = 0.82

9. Example - Higher 3D Sim 141 2D sim = 0.2 3D sim = 0.7 454

10. Spark’s Approach Rofecoxib Valdecoxib Etoricoxib 12 nM > Find bioisosteres by replacing sections of the molecule

11. Spark’s Approach 1Select a region to replace and remove these atoms

12. Wrong distance Spark’s Approach 1Select a region to replace and remove these atoms 2Search database for matching fragments (geometric search only) (search runs on fragment conformations)

13. Spark’s Approach Wrong angle 1Select a region to replace and remove these atoms 2Search database for matching fragments (geometric search only) (search runs on fragment conformations)

14. 1Select a region to replace and remove these atoms 2Search database for matching fragments geometric search only (search runs on fragment conformations) 3Form Products minimise and add field points Spark’s Approach Good match

15. 1Select a region to replace and remove these atoms 2Search database for matching fragments geometric search only search runs on fragment conformations 3Form Products minimise and add field points 4Score Spark’s Approach 0.88

16. > Produces more diverse, non- obvious bioisosteres > Avoids fragment scoring limitations > Allows for electronic influence of replacing a moiety on the rest of the molecule and vice versa > Allows for neighbouring group effects Whole-Molecule Scoring Advantages

17. Example - COX-2 > Search for Bioisosteres for cyclic lactone of Rofecoxib Actives: 9 of the first 10 clusters 21 of the first 30 clusters Search Common Dbs 87,225 frags

18. Cluster, Result Nos Cluster id FieldStere result 2D simclosest lit compd 10,120.52Same, 60nM 13,190.509 7nM 32, 104 0.48None COX-2 Results Cluste r, Result Nos Cluster id SPARK result2D sim closest lit compd 1,1 0.64 6 2,2 0.53 1 6.5uM 5,5 0.50 0 Same, 10nM 9,11 0.53 2 70nM

19. Scaffold replacement ‘Sildanafil’ spark (10 mins)NEAT? spark results 2-5 Fsim score0.985 0.9820.978 spark results 6, 7, 10, 13 Fsim score0.973 0.9590.957 spark results 14, 18, 26, 30 Fsim score0.9530.9510.9430.939 Pfizer J. Chem. Inf. Model. 2012

20. Fragment growing example > FieldStere version 3.0.0 fragment growth example: 1.P38 kinase bound to a fragment fluorescent probe PDB:3K3I specific to the ‘DFG-out’ conformation 2.‘DFG-in’ example with specificity towards the ‘Gly’ flipped hinge PDB:3ROC and/or 3HUB > Selectivity potentially to be gained by combining ‘Gly flip’ and ‘DFG-out’ in one molecule > Can we use the new version of SparkV10 to grow the DFG-out fragment into the DFG-in hinge?

21. Fragment in DFG-out pocket, PDB:3K3I predominant hinge conformation Graphics from Pymol from Delano Scientific

22. +Gly hinge flip ligand_1, PDB:3ROC Hinge Gly flip Graphics from Pymol from Delano Scientific

23. Fragment compatibility – DFG-out

24. Fieldstere output: 2D mols

25. Fieldstere output: 3D mols and fields Fragment and referenceRank 4Rank 6 Rank 11 Rank 13Rank 53

26. Outcome > Fragment growth both possible and a facile using an automated process with SparkV10 > Interesting and sensible candidate molecules generated > Predict highly selective p38 actives > Absolute requirement for 3D insight

27. Any relevance? – Pfizer compound for COPD Deposited in PDB: 2YIS November 2011 Clinical trials for COPD Virtual compounds in the output list……prepared for ACS San Diego Late Summer 2011

28. Conclusion > Cresset offer a wide variety of software and collaborative solutions for drug discovery > Cutting edge technology > Provide key insights

29. martin@cresset-group.com Questions welcomed

30. COX-2 Results

31. Product Space TargetResult 5Result 1,484

32. +Gly hinge flip ligand_2, PDB:3HUB Hinge Gly flip