Biomolecular simulations. PRACTICAL 2.

INTRODUCTION:
In this tutorial, you will be introduced to the docking approaches by undertaking on your
own some docking experiments of different ligands on the androgen binding receptor seen
in the Practical 1. The goal is to predict the structure of the complexes and estimate their
binding free energies. The different steps of the work are summarize below.

Wi will use UCSF Chimera to prepare the structure of the receptor and the ligands, and to
create the inputs files for Autodock Vina. The latter is the program to be used to run the
docking calculations. YOU HAVE TO DOWNLOAD AND INSTALL BOTH PROGRAMS.

LIGAND: Testosterone (TES) PDB: 2am9

Natural androgen

PROTEIN: Human androgen receptor.

WHAT YOU HAVE TO DO:

Docking TES to the AR structure 2am9 = Prep structures + docking + analysis (see
points bellow)

1. PREPARING THE STRUCTURES FOR DOCKING:

In Chimera, we need to prepare first the two structures independently: the ligand and
the receptor. To do so, following with what you learned during the previous day:
 open the 2am9 structure
 remove all ligands and water molecules (solvent)

 Note 1: Gln711 presents two conformations in PDB. Select only one (the one
able to interact with a bound ligand).
 once cleaned use the dock prep interface (Tools –> Surface/Binding Analysis –>
DockPrep) to add hydrogen and clean any other possible problems (i.e.
rotameric states, etc…)
 then save the mol2 of the resulting receptor (i.e. with name receptor.mol2) and
also its pdb file for future use (receptor.pdb)

Proceed the same way with the ligand (this time start by removing all the atoms of the
protein, solvent, other ligands and only keep the testosterone, e.g. select :TES; delete
~selection).

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CAUTION!!: check protonation of TES as chimera does it wrong. It puts an extra H
atom. Delete in in Chimera. Then run a second time DockPrep for the ligand
WITHOUT ADDING hydrogens.
The reason for that is that it assigns type O.3 to carbonyl O of TES. In the saved mol2
file, with a text editor (e.g. Word Pad), change this O.3 to O.2. Also indicate (@BOND
section) that this O makes a double bond with the C.
We also need to change the HO17 atom to H18 (I’ll explain that). Save the new mol2.

2. GENERAL DOCKING SCHEME IN CHIMERA WITH VINA:

Receptor: apply DockPrep and

Load cleaned save mol2 file Visualize/
receptor and Launch analize results
Ligand: addH, check they are Vina
ligand ; and save
correct, minimise structure, docking
separate PDB Chimera
apply DockPrep (no-addH
files session
here) and save mol2 file and
correct

Once both mol2 files have been generated, open them back in a new Chimera session.

Then go to the Surface/Binding analysis Menu and select the Autododock Vina entry.
A new window pops up. There, select the name of the output file, the ligand and the
receptor. Double check that you correctly selected the right models for both receptor
and ligand!

Finally, you have to define/delimit the region of the space where the calculation will be
performed. To do so, use the 3D handling of the mouse (middle button) for the protein
region.
Note 2: As a reference, you may use something like: Box centre: 26.5, 2.5, 4.5 Å
Box size: 18 x 20 x 18 Å.
Save the session once you get the results!!!

ANALYSIS: Once the calculation ends, a window will appear with the results of the
docking. Open back the original structure and compare the predicted versus the
original structures.
Note 3: When analysing the docking results, look at the affinity prediction given by
Vina and the possible protein-ligand interactions (H-bonds and hydrophobic
contacts) in the best model predicted by Vina.

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**The docking result should be independent on the initial geometry. If you have
time, try adding +5.0 to all x coordinates of TES in the mol2 file and repeat the
docking calculation.

REPORT: Provide a 2 pages report with a brief summary of what has been done and
the results obtained (with good quality images).