1. Privileged Substructures Revisited: Target Community-Selective Scaffolds Jürgen Bajorath Life Science Informatics University of Bonn

2. Privileged Substructures  First postulated by Evans et al. in 1988 based on the observation that many cholecystokinin antagonists contained conserved substructures not frequently seen in other active compounds  Since then the search for target class-privileged chemotypes has continued in medicinal chemistry  Generally accepted definition : - Recurrent fragments in ligands of a given target family - Selective at the family level, but not for individual targets Evans BE et al. J. Med.Chem.1988, 31, 2235-2246

3. Privileged Substructures  Existence of truly target family-privileged substructures has remained controversial  Intrinsic limitation: Search for privileged substructures has been based on frequency of occurrence analysis of pre- selected substructures  Often drawn conclusion: Substructure might occur with high frequency among ligands of a particular target family but also act on other families

4. Schnur DM et al. J. Med. Chem. 2006, 31, 2000-2009 Target Family Set# Compounds# Substructures GPCR class A216201190 Ligand gated ion channels 3792297 Nuclear hormone receptors (NHRs) 2176121 Protein kinases1079101 Serine proteases3015323 Privileged Substructures Are target family-privileged substructures truly privileged?

5. Schnur DM et al. J. Med. Chem. 2006, 31, 2000-2009 Target Family Substructure Sets Ligand sets GPCR Ion channels NHRs Protein kinases Serine proteases Random cpd sets GPCR class A-26%10%11%17%46% Ligand gated ion channels 47%-15%19%92%99% Nuclear hormone receptors (NHRs) 40%30%-17%15%45% Protein kinases48%34%16%-20%57% Serine proteases25%11%7%91%-37% Privileged Substructures Are target family-privileged substructures truly privileged?

6. Changing the Analysis Concept  Do molecular scaffolds exist that exclusively occur in ligands of individual target families ? - Bemis & Murcko framework (scaffold) - Large-scale distribution in target families Peptidases Kinases GPCRs...  Departing from frequency of occurrence analysis of pre- selected substructures  Systematic compound data mining taking all available activity annotations into account

7. Hierarchical Scaffolds Bemis GW and Murcko MA. J. Med. Chem.1996, 39, 2887-2893 Compound R-groupsFramework Ring System Linker 1 2 3

8. Public Data Source - BindingDB  BindingDB database: - Public repository of activity information of small molecules - ~31,000 compound entries with ~57,000 activity annotations - 17,745 compounds active against human targets extracted

9. Analysis Strategy - Compound Sets  Target pair sets: - Active compounds are organized into target pair sets - A set contains all compounds active against two individual targets (i.e. compounds might belong to multiple sets)  Binding DB target pair sets: - Sets obtained for 520 pairs of targets that share >= 5 compounds - 6,343 compounds active against 259 human targets  Pubchem confirmatory bioassays: - Only 3 relevant human target pairs meet the >= 5 compound criterion

10. Compound-Based Target Network  520 target pairs are visualized in a network representation - Nodes: targets - Edges: target pair sets - Edge width: number of shared compounds  Densely connected communities - 18 communities - >= 4 targets - Different target families 1 2 34 56 78 9101112131415161718 Ser/Thr kinases Serine proteinases Caspases Tyrosine kinases MMPs & CAs

11. Community-Selective Scaffolds  520 human target pair sets (6,343 BDB compounds; 259 targets); 18 target communities  206 community-selective scaffolds: - Exclusively act in a single community - With 5 - 45 compounds/scaffold (av. ~12) - Yielding 147 distinct carbon skeletons (topological diversity)

12. Adding Selectivity Information  For each compound active against a target pair, its target selectivity (TS) is calculated as:  Compound |TS| values range from 0 to 6.86 - 0: equal potency, no selectivity - 6.86: potency difference of nearly 7 orders of magnitude, i.e. highly selective for one target over another  Selectivity profiles of scaffolds - Community-based - Target-based

13. Selectivity Profiles  Community-based selectivity profile: - For each scaffold found in a given community  All corresponding compounds active against any target pair in this community pooled  Median of their absolute TS values determined (median |TS|)  Target-based selectivity profile: - For each scaffold active against a given target  All corresponding compounds active against this target pooled  Selectivity against any other target calculated  Median of their TS values determined (median TS)

14. Community Selectivity of Scaffolds  Scaffold / Community heat map: - Columns: target communities - Rows: scaffolds - Color spectrum: median |TS|  Red: scaffold yields many compounds with different potency against individual targets  Yellow: scaffold does not yield selective compounds  Non-selective scaffolds - Occur in multiple communities  Community-selective scaffolds - Exclusively occur in one community

15. Target Selectivity of Scaffolds  Scaffold / Target heat map: - Columns: targets in a community - Rows: scaffolds - Cell: the scaffold represents >= 5 compounds active against the target - Color spectrum: median TS  Red (positive): more selective for the target over others in the community  Yellow (negative): more selective for other members of the community

16. Target Selectivity of Scaffolds  Different scaffolds display same selectivity profile - e.g. Factor Xa/Thrombin  Scaffolds with no apparent target selectivity  Number of scaffolds per target varies - Factor Xa: 17; Thrombin: 18 - Tryptase: 0; Hepsin: 0 Community 3: 16 serine proteases

17. Target Selectivity Ranking  Community-selective scaffolds are ranked according to median |TS| 5.2 0 1 2 111 scaffolds with target- selective tendency 37 scaffolds at least half of compounds having >= 100-fold potency differences against >= 2 community targets

18. Community-Selective Scaffolds DPP4 DPP8 CA1 CA5A CA5B CA6 CA4 CA9 CA2 CA14 CA12 CA7 CA3 98: 1.10 3: 4.03 Rank Median |TS| Color spectrum: median TS Red: high potential to yield target-selective compounds Yellow: low potential

19. Selectivity Searching (MDDR) Thrombin FXa Highly selective for FXa over other serine proteases

20. Caspase 7 Caspase 3 Selectivity Searching Inhibit both caspase 3 and 7 with nM potency; ~200-fold selective over caspases 1, 6, 8

21. Extending the Analysis: ChemblDB  Recent public domain database: ChemblDB - ~500,000 compounds with activity information - 32,848 compounds with high-confidence annotations active against 671 human targets  High-confidence activity annotations: - Target confidence level: 9 - Interaction type: D(irect) ftp://ftp.ebi.ac.uk/pub/databases/chembl/latest/

22. - Active compounds (human targets) - Scaffolds - Network - Community-selective scaffolds - Topologically distinct scaffolds ChemblDB vs. BindingDB  Comparison at different levels 32,848 ChemblDB 17,745 BDB 3,589 12,902 ChemblDB 6,291 BDB 1,409 CompoundsScaffolds

23. - Active compounds (human targets) - Scaffolds - Network - Community-selective scaffolds - Topologically distinct scaffolds ChemblDB vs. BindingDB  Comparison at different levels BDB CDB shared targets unique targets tyrosine kinases GPCRs

24. - Active compounds (human targets) - Scaffolds - Network - Community-selective scaffolds - Topologically distinct scaffolds ChemblDB vs. BindingDB  Comparison at different levels 311 ChemblDB 206 BDB 34 227 ChemblDB 147 BDB 85 Community-selectiveTopologically distinct

25. Community-Selective Scaffolds  Distribution in drugs? - DrugBank: 1,247 approved drugs with 726 unique scaffolds - Only 11 overlap with 206 community-selective BDB scaffolds - Community-selective scaffolds currently underrepresented in drugs; opportunities for further chemical exploration

26. Conclusions  The existence of target class-privileged substructures has remained controversial over the years  From putative privileged substructures to confirmed target community-selective scaffolds through systematic data mining  Community-seletive scaffolds are abundant and topologically diverse  A subset of community-selective scaffolds displays a notable tendency to produce compounds with different target selectivity  BDB and CDB contain complementary target and scaffold information

27. Acknowledgments Ye Hu Anne Mai Wassermann Eugen Lounkine