113 Docking tutorial Esther Kellenberger Facult de Pharmacie

1/13 Docking tutorial Esther Kellenberger Faculté de Pharmacie UMR 7200, Illkirch Tel: 03 68 85 42 21 e-mail: ekellen@unistra. fr

workflow goal material Exercise 1 Exercise 2 Exercise 3 The docking workflow Ligand preparation • • standardization (aromatization, ionisation, tautomer) generation of a low energy conformer Protein preparation • • receptor and binding site definition structure check - ionisation state GLU, ASP, HIS, LYS, ARG - tautomeric state HIS - position of the polar hydrogen atoms (SER, TYR, THR, LYS, ASN, GLN) - crystal water molecules - metal coordination type - addition of hydrogen atoms Docking and scoring Results are the structure file of the best ligand poses and the score of each pose 2/13

workflow goal material Exercise 1 Exercise 2 Exercise 3 3/13 Understanding the docking paradigm 1. Re-docking Exercice E 1: re-docking of tacrine back into its co-crystal receptor - effect of the ligand ionisation - effect of the water in binding site Ligand docking PDB complex predicted complex Receptor Investigated issues: The quality of ligand protein preparation impacts the docking outcome Docking requires expert intervention to predict unusual binding mode

workflow goal material Exercise 1 Exercise 2 Exercise 3 4/13 Understanding the docking paradigm 2. Cross-docking Exercice E 2: cross-docking of tacrine-hupyridone inhibitor (A 2 E) and aricept (E 20) into the binding site of tacrine(TAH)-bound acetylcholinesterase PDB complex #2 PDB complex #1 Ligand docking predicted complex Receptor Investigated issues: Ligand protein binding site flexibility

workflow goal material Exercise 1 Exercise 2 Exercise 3 Understanding the docking paradigm 3. Screening Exercice E 3: screening docking of DUD dataset into the binding site of tacrine(TAH)-bound acetylcholinesterase, ranking the compounds to discriminate true binders from decoys cpds# 1121 222 3563 578 639 actives ΔGbind -44. 51 -42. 21 -41. 50 -40. 31 -40. 28 … 670 +22. 54 Investigated issues: The limited accuracy of scoring functions 5/13

workflow goal material Exercise 1 Exercise 2 Exercise 3 Lead. IT / Flex. X Quickstart Protein preparation Receptor >> Load or prepare. . . Select the protein PDB file and follow the instructions Ligand preparation Docking >> Choose Docking Library. . . Load the MOL 2 file Move the 'preparation' from default to ‘off’. Docking >> Define Flex. X Docking. . . 6/13

workflow goal material Exercise 1 Exercise 2 Exercise 3 Course material Input pdb 1 acj. ent PDB entry receptor acj_WAT. mol 2 1 eve_ali_WAT. mol 2 prepared receptor Ligand neutral tacrine (+) charged tacrine-hupyridone inhibitor aricept D. U. D Ach. E dataset TAH_1 acj. mol 2 TAH_1 acj+. mol 2 A 2 E_1 zgc. mol 2 E 20_1 eve. mol 2 DUD. mol 2 Flexx (1 acj) (1 eve) (1 acj) (1 zgc) (1 eve) mol 2/sdf/csv/fxx result files exercise E. 1. 1 acj_TAHsite 65_TAHredock 1 acj_TAHsite 65_TAH+redock 1 acj_TAHsite 65 WAT_TAH+redock exercise E. 2. 1 acj_A 2 Esite 65 WAT-A 2 Ecrossdock 1 acj_E 20 site 65 WAT-E 20 crossdock 1 eve_E 20 site 65 WAT_E 20 redock exercise E. 3 1 acj_A 2 Esite 65 WAT_DUDscreening Output, full projects 7/13

workflow goal material Exercise 1 Exercise 2 Exercise 3 8/13 Exercise E. 1: Re-docking tacrine (TAH) back into the acetylcholinesterase binding site The tacrine / acetylcholinesterase binding mode of is difficult to predict. PDB 1 acj complex shows: • pocket size >> ligand volume • only one polar intermolecular interaction • two key water molecules

workflow goal material Exercise 1 Exercise 2 Load tacrine / acetylcholinesterase 1 acj PDB complex Exercise 3 9/13 input/pdb 1 acj. ent Prepare the receptor and define a 6. 5 A site around tacrine Dock the neutral tacrine (TAH) / positively charged tacrine (TAH+) Input/ligand/TAH_1 acj. mol 2 Input/ligand/TAH_1 acj+. mol 2 PDB ligand repository Harel et al. (1993) Proc Natl Acad Sci U S A. Include water in the receptor, dock TAH+ Docking accuracy for the docking ensemble (10 poses per ligand) pdb_ligand_site ligand 1 acj_TAH_site 65 TAH Only wrong solutions: Ligand up-side-down 1 acj_TAH_site 65 TAH+ Mixture of correct and wrong poses 1 acj_TAH_site 65_WAT TAH+ Only correct poses

workflow goal material Exercise 1 Exercise 2 Exercise 3 10/13 Exercise E. 2: Cross-docking A 2 E and E 20 into TAH-bound acetylcholinesterase Tacrine-hupyridone inhibitor (A 2 E) - is a derivative of tacrine (TAH+) - is more flexible than tacrine (TAH+) A 2 E TAH+ The tacrine substructure of the A 2 E is correctly placed in the protein pocket. The docking of A 2 E pyridone group is hindered by unsuitable W 279 rotamer.

workflow goal material Exercise 1 Exercise 2 Exercise 3 The E 20 inhibitor is not chemically similar to TAH / A 2 E. The docking of E 20 is prevented by unsuitable F 330 rotamer. The E 20/ acetylcholinesterase binding mode of is difficult to predict, because: • both ligand binding site contain polar and charged groups • BUT no H-bonds nor ionic bonds are experimentally observed in the X-ray complex X-ray Re-docking 11/13

workflow goal material Exercise 1 Exercise 2 Exercise 3 12/13 Exercise E. 3: Screening the DUD dataset, using TAH-bound acetylcholinesterase The DUD dataset 107 true binders and 3892 decoys. strong bias in the active set (towards E 20 derivatives) Huang, Shoichet and Irwin in 2006 (DOI 10. 1021/jm 0608356) Don’t start the calculation (~2 days/1 cpu)! Top 1% Top 20% True positive (ACTIVE) rate, TPrate …. / 107 = False positive (DECOYS) rate, FPrate …. / 3892 = Enrichment factor (TPnumber / 40) ---------- = (107 / 3999) (TPnumber / 800) ---------- = (107 / 3999) Enrichment factor from Huang et al. 1. 9 2. 0

workflow goal material Exercise 1 Exercise 2 Exercise 3 13/13 Poor docking accuracy true binders not correctly docked Poor scoring accuracy in ranking compounds high score of decoys due to irrelevant polar interaction Impossible identification of the true actives? acetylcholinesterase is a “difficult” target for docking half of active compounds are similar to E 20, and can not be accurately docked the decoys are challenging Expert intervention slightly increases the screening performance.