Docking and Cancer Drug Design

1. Docking and Cancer Drug Design Jennie Bever

2. Where to start? • Ligand (analog-based) • Target (structure-based)

3. Goals of Docking • Characterize binding site - make an image of binding site with interaction points • Orient ligand into binding site - grid search - descriptor mapping - energy search • Evaluate strength of the interaction DG bind= DG complex – (DGligand + DGtarget)

4. Structure-based design of selective and potent G quadraplex-mediated telomerase inhibitorsNeidle et al. 2001 PNAS 98(9) 4844-4849 NMR-derived G4 structure PDB entry 143D Repeat of d[AG3(TTAG3)3]

5. Telomerase • Activated in 80-90% human tumors • Keeps cancer cells’ telomeres stable length

6. Telomerase as a Drug Target • Telomerase needs single stranded 3’DNA primer end • To hybridize with telomerase RNA template • Drug Target: • Use higher order structure to prevent telomeres from unfolding • No ss primer • Block telomerase

7. G quadraplex Telomere repeat d[AG3(TTAG3)3] G repeats form H bonds quadraplex

8. Stabilize Quadraplex– How? • Extended planar aromatic chromophore • Nearly all known quadraplex ligands share this structure

9. Problems with known ligands • Affinity for duplex DNA comparable to quadraplex binding • Low potency for telomerase inhibition IC50=2-5mM • Level of acute cytotoxicity too high

10. From Structure to Ligand 1) Energy minimize structures of target and ligand Molecular dynamics simulation  time averaged structures 3) Create pseudointercalation binding site

11. Docking • Dock ligand into pseudo-intercalation site • Manual, automatic, and flexible ligand docking • Energy minimize to determine DG complex • Determine DGligand _=interaction energy of ligand with surroundings when explicitly solvated

12. Visual inspection of compound 1 docking • Compounds 3 and 4 • Similarly docked

13. Docking results • Attempts at docking compound 2 were unsuccessful • Distorted the quadraplex structure due to bulky side chains

14. Ligand/quadraplex interactions in solution: SPR Rate constant determination

15. Ligand/quadraplex interactions in solution:SPR Equilibrium constant determination

16. Will these molecules work?Trap Assays and Growth Inhibition (Cytotoxicity)

17. Docking-based Development of Purine-like Inhibitors of Cyclin-Dependent Kinase-2Koca et al. J. Med. Chem. 2000, 43, 2506-2513 Cdk2 structure complexed with ATP Cdk2 regulates G1/S transition Cdk deregulation in many tumors and tumor cell lines

18. Xray structures of 3 cdk2 complexes available • ATP, olomoucine, roscovitine • All bind in same cleft, but with different orientations

19. Docking of 2,6,9-purine derivatives into cdk2 • Minimize structures (target and ligands) • Represent active site as spheres • Calculate partial atomic charges from force fields • Rigid docking  Pick receptor structure to use • Rigid and Flexible docking with proposed ligands

20. Interaction energy and Inhibitory potency (IC50) for 2,6,9-purine derivatives on cdk1 and cdk2 They say good correlation for cdk2 interaction energy can be used to predict activity

21. Interaction energy versus IC50 For cdk1, rank of activities also closely bounded to rank of interaction energies

22. Searching for New Inhibitors

24. Role of Electrostatic and van der Waals contribitions in binding ligand to active site

25. H bonds predicted by rigid docking agree with experimental data

26. How well does docking compare to crystal structure? 2 binding modes found  roscovatine-like—agreed very well with crystal structure  ATP-like—differences in the orientation of N9 isopropyl and C2 side chain shape

27. Fix C2 and isopropyl to be rigid—repeat docking

28. Paper Conclusions: • Rigid docking useful for activity predictions • Relationship between cdk1 activity and cdk2 interaction energy • Use these experiments to design new inhibitors of cdk2 and cdk1

29. My Conclusions • Docking is now and will be an integral tool in drug design in the future • Play with some of the modeling software—it’s cool!—and helps to understand how simulations are done • Thanks to Dr. Bourne!