Docking tutorial

G. Marcou1, E. Kellenberger2

1Faculté de Chimie, UMR7140

2Faculté de Pharmacie, UMR 7200, Illkirch

1/13

Exercise1

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

The docking workflow

material 2/13 workflow Exercise 2 Exercise 3 goal

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

Investigated issues:

The quality of ligand and protein preparation impacts the docking outcome

Docking requires expert intervention to predict unusual binding mode

Exercise1 goal 3/13 workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

Ligand

Receptor

PDB complex

docking predicted complex

Exercice E2: cross-docking docking of tacrine-hupyridone inhibitor (A2E) and aricept (E20) into the binding site of tacrine(TAH)-bound acetylcholinesterase

Investigated issues:

Ligand and protein binding site flexibility

Understanding the docking paradigm

2. Cross-docking

Exercise1 goal 4/13 workflow Exercise 2 Exercise 3 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

Ligand

Receptor

PDB complex #2

docking

PDB complex #1

predicted complex

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.

Investigated issues:

The limited accuracy of scoring functions

actives

S

S

Br

O

O

NH

H

O S

S

Br

O

O

NH

H

OS

S

Br

O

O

NH

H

O

S

S

Br

O

O

NH

H

O

decoys cpds# ΔGbind

1121 -44.51 222 -42.21

3563 -41.50

578 -40.31

639 -40.28

…

670 +22.54

Exercise1 goal 5/13 workflow Exercise 2 Exercise 3 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

LeadIT / FlexX Quickstart

6/13

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...

Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

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

Flexx mol2/sdf/csv/fxx result files

exercise E.1. 1acj_TAHsite65_TAHredock

1acj_TAHsite65_TAH+redock 1acj_TAHsite65WAT_TAH+redock

exercise E.2. 1acj_A2Esite65WAT-A2Ecrossdock

1acj_E20site65WAT-E20crossdock 1eve_E20site65WAT_E20redock

exercise E.3 1acj_A2Esite65WAT_DUDscreening

7/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

Output, full projects

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

8/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

Exercise E.1: Re-docking tacrine (TAH) back

into the acetylcholinesterase binding site

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+) Include water in the receptor, dock TAH+

pdb_ligand_site ligand Docking accuracy for the docking ensemble

(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

9/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

Input/ligand/TAH_1acj+.mol2

Harel et al. (1993)

Proc Natl Acad Sci U S A.

Input/ligand/TAH_1acj.mol2

PDB ligand

repository

10/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

Tacrine-hupyridone inhibitor (A2E)

- is a derivative of tacrine (TAH+)

- is more flexible than tacrine (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.

Exercise E.2: Cross-docking A2E and E20 into

TAH-bound acetylcholinesterase

A2E

TAH+

X-ray Re-docking

11/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

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

Top 1% Top20%

True positive (ACTIVE) rate, TPrate …. / 107 = …. / 107 =

False positive (DECOYS) rate, FPrate …. / 3892 = …. / 3892 =

Enrichment factor (TPnumber / 40) ------------------- = (107 / 3999)

(TPnumber / 800) ------------------- = (107 / 3999)

Enrichment factor from Huang et al. 1.9 2.0

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% Top20%

True positive (ACTIVE) rate, TPrate …. / 107 = …. / 107 =

False positive (DECOYS) rate, FPrate …. / 3892 = …. / 3892 =

Enrichment factor (TPnumber / 40) ------------------- = (107 / 3999)

(TPnumber / 800) ------------------- = (107 / 3999)

Enrichment factor from Huang et al. 1.9 2.0

12/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

13/13 Exercise1 goal workflow Exercise 2 Exercise 3 Exercise1 material workflow Exercise 2 Exercise 3 goal

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.