1. Free Energy Calculations in Drug Discovery Seminar Course by Dr. Avraham Samson Tomer Meirson MD-PhD student

2. Introduction – Free Energy of Gibbs 2

3. 3 Introduction – Free Binding Energy Potential Energy A + B A --- B AB

4. Overview – Measuring Affinity Experimentally 4 SPR – Surface Plasmon Resonance ITC – Isothermal Titration Calorimetry FP – Fluorescence Polarization

5. Overview – Measuring Affinity Computationally 5 Molecular Docking No dynamics No solvent ∆G calculation Dynamic Implicit solvent ∆G calculation Dynamic Explicit solvent ∆∆G calculation FEP – Free Energy of Perturbation MM/GBSA – Molecular Mechanics General Born Surface Area

6. Why FEP? Current computational methods are good for posing but bad for assessing the affinity 6

7. Objectives – FEP Development 7 Accurate estimation of binding affinity Alternative to biochemical assays Massive synthesis Can be avoided Enhanced Drug Discovery

8. Methods - FEP 8

9. Combinatorial Chemistry 9 In combinatory chemistry an unlimited number of molecular constructions can be made FEP uses “alchemical” technique in which one molecule transforms gradually into another in order to calculate the relative binding energy accurately

10. Alchemistry 10

11. Method – Alchemistry and the Abstract Lambda 11

12. Results – FEP representatives 12

13. Results 13

14. Results 14

15. Protein FEP for Mutation Resistance 15

16. FEP Requirements and Limitations 16

17. FEP Requirements and Limitations 17

18. Conclusions 18

19. Acknowledgment 19

20. Questions ? 20