1/13 Docking tutorial G. Marcou 1 , E. Kellenberger 2 1 Faculté de Chimie, UMR7140 2 Faculté de Pharmacie, UMR 7200, Illkirch
2/13 workflow goal material Exercise1 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
3/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Understanding the docking paradigm 1. Re-docking Exercice E1: re-docking docking of tacrine back into its co-crystal receptor - effect of the ligand ionisation - effect of the water in binding site Ligand docking PDB predicted complex complex Receptor Investigated issues: The quality of ligand and protein preparation impacts the docking outcome Docking requires expert intervention to predict unusual binding mode
4/13 workflow workflow workflow goal goal goal material Exercise1 Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Exercise 3 Understanding the docking paradigm 2. Cross-docking Exercice E2: cross-docking docking of tacrine-hupyridone inhibitor (A2E) and aricept (E20) into the binding site of tacrine(TAH)-bound acetylcholinesterase PDB Ligand complex #2 docking predicted PDB complex complex #1 Receptor Investigated issues: Ligand and protein binding site flexibility
5/13 workflow workflow workflow goal goal goal material Exercise1 Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Exercise 3 Understanding the docking paradigm 3. Screening Exercice E3: screening docking of DUD dataset into the binding site of tacrine(TAH)-bound acetylcholinesterase, ranking the compounds to discriminate true binders from decoys. decoys cpds# Δ G bind Br Br 1121 -44.51 S Br O O S 222 -42.21 S O O O 3563 -41.50 S S Br O H N O O 578 -40.31 S H actives O H N S 639 -40.28 H O O H N S O … H 670 +22.54 H N H Investigated issues: The limited accuracy of scoring functions
6/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 LeadIT / FlexX Quickstart Protein preparation Molecules >> Prepare Receptor... Select the protein PDB file and follow the instructions Ligand preparation Molecules >> Choose Library... Load the MOL2 file Do not tick the box Protonate as in aqueous solution ( for exercise purpose ). Docking Docking >> Define FlexX Docking...
7/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Course material Input pdb pdb1acj.ent PDB entry (1acj) receptor acj_WAT.mol2 prepared receptor (1acj) 1eve_ali_WAT.mol2 prepared receptor (1eve) Ligand TAH_1acj.mol2 neutral tacrine (1acj) TAH_1acj+.mol2 (+) charged tacrine (1acj) A2E_1zgc.mol2 tacrine-hupyridone inhibitor (1zgc) E20_1eve.mol2 aricept (1eve) DUD.mol2 D.U.D AchE dataset F lexx mol2/sdf/csv/fxx result files exercise E.1. 1acj_TAHsite65_TAHredock 1acj_TAHsite65_TAH+redock Output, 1acj_TAHsite65WAT_TAH+redock exercise E.2. 1acj_A2Esite65WAT-A2Ecrossdock full projects 1acj_E20site65WAT-E20crossdock 1eve_E20site65WAT_E20redock exercise E.3 1acj_A2Esite65WAT_DUDscreening
8/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Exercise E.1: Re-docking tacrine (TAH) back into the acetylcholinesterase binding site The tacrine / acetylcholinesterase binding mode of is difficult to predict. PDB 1acj complex shows: • pocket size >> ligand volume • only one polar intermolecular interaction • two key water molecules
9/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Load tacrine / acetylcholinesterase 1acj PDB complex input/pdb/pdb1acj.ent Prepare the receptor and define a 6.5A site around tacrine Dock the neutral tacrine (TAH) / positively charged tacrine (TAH+) Input/ligand/TAH_1acj.mol2 Input/ligand/TAH_1acj+.mol2 PDB ligand Harel et al. (1993) Proc Natl Acad Sci U S A. repository Include water in the receptor, dock TAH+ Docking accuracy for the docking ensemble pdb_ligand_site ligand (10 poses per ligand) 1acj_TAH_site65 TAH Only wrong solutions: Ligand up-side-down 1acj_TAH_site65 TAH+ Mixture of correct and wrong poses 1acj_TAH_site65_WAT TAH+ Only correct poses
10/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 Exercise E.2: Cross-docking A2E and E20 into TAH-bound acetylcholinesterase Tacrine-hupyridone inhibitor (A2E) - is a derivative of tacrine (TAH+) - is more flexible than tacrine (TAH+) A2E TAH+ The tacrine substructure of the A2E is correctly placed in the protein pocket. The docking of A2E pyridone group is hindered by unsuitable W279 rotamer.
11/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 The E20 inhibitor is not chemically similar to TAH / A2E. The docking of E20 is prevented by unsuitable F330 rotamer. The E20/ acetylcholinesterase binding mode of is difficult to predict, because: • both ligand and 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
12/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 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 E20 derivatives) Huang, Shoichet and Irwin in 2006 (DOI 10.1021/jm0608356) Don ’ t start the calculation (takes more than 5 hours)! Top 1% Top 1% Top20% Top20% True positive (ACTIVE) rate, TPrate True positive (ACTIVE) rate, TPrate …. / 107 = …. / 107 = …. / 107 = …. / 107 = False positive (DECOYS) rate, FPrate False positive (DECOYS) rate, FPrate …. / 3892 = …. / 3892 = …. / 3892 = …. / 3892 = Enrichment factor Enrichment factor (TPnumber / 40) (TPnumber / 40) (TPnumber / 800) (TPnumber / 800) ------------------- = ------------------- = ------------------- = ------------------- = (107 / 3999) (107 / 3999) (107 / 3999) (107 / 3999) Enrichment factor from Huang et al. 1.9 2.0 Enrichment factor from Huang et al. 1.9 2.0
13/13 workflow workflow goal goal material Exercise1 Exercise1 Exercise 2 Exercise 2 Exercise 3 Exercise 3 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 E20, and can not be accurately docked the decoys are challenging Expert intervention slightly increases the screening performance.
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