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Ligand Docking
The procedure finds the position of a small molecule in the active site
of a given protein with the minimum value of the free binding energy and predicts
the IC50 of the ligand.
BACKGROUND: The Ligand Docking Module requires 3D structures of a
protein and a ligand. The position of the active site of the protein should be
known. Protein structures can be downloaded from the Protein Data Bank, as well
as from some other sources of 3D biological macromolecular structure data. The
ligand structure can be drawn by using the Edit->Move/Build option
of the Main
After selecting Tools->Ligand docking, the following
procedures will take place.
Selecting a Small Molecule for
Docking
choose a small molecule for docking by clicking on it.
You can make it by using both the 3D structure (Figure 25) (b) and the
1D structure (a).
Figure 25 - Small Molecule Selection
After selecting a ligand, the viewer zooms in on the ligand and shows
the molecule in sticks.
Press the Next button in the Wizard (c) to proceed with the
following steps.
Setting the Protonation State and Adding Explicit
Hydrogen atoms to the Ligand
BACKGROUND: Most sources of 3D structures provide molecules only with
heavy atoms and without hydrogen atoms. There is also no information on bond
types (single, double etc.) and protonation state (adding or extracting a
hydrogen atom depending on the pH and the chemical group). But it is essential
for Quantum's calculations to have the right number of hydrogen atoms in
molecules. This procedure helps to do this.
The small molecule, which was selected in the previous step, is added as
a separate object under the name "ligand" (Figure 26) (b).
The notice on the display (a) informs you that you should fix hydrogen
atoms and bond types.
Figure 26 - The Ligand
·
Go to the next step if you think
the ligand has the right number of hydrogen atoms.
·
Use the Build Model option (c) from
Wizard to set the protonation state and add hydrogens by using Quantum's
algorithms.
·
Use Builder (Figure 27) to manually
set bond types and add/remove hydrogen atoms.
Figure 27 - Builder
Use options (a) to deliver hydrogens and (b) to change the number of
bonds. To do this , you should use the atom selection (left click) and the
bond's selections (right click). You can find more information on working with
Builder in the section Moving and
Building Molecules.
Note: We recommend that you use the Build
Model option. Build Model analyses the geometry of the molecule -
bond lengths and bond and dihedral angles - and adds missing hydrogen atoms.
The Build Model procedure also sets the right protonation states (Figure 28).
Figure 28 - Fixing the Ligand
Note: However, you should take into
account that in some cases that molecules from the Protein Data Bank do not
have the right geometry, and you have to fix them without the assistance of the
Build Model procedure or, you have to at least manually correct them after
Build Model.
Building
a Grid box in the Active Site
BACKGROUND: Whenever the ligand position inside the active site is not
known, the program uses optimization to minimize the binding free energy using
Quantum's advanced energy evaluation algorithm. The recommended way to speedup
the calculation is to employ precalculated potentials stored in the grids. A
grid is a 3D box (gridbox) characterized by three orthogonal directions and its
size.
In order to construct a grid box, the following requirements should be
met:
·
All active site atoms should be
covered by a grid box, or at least all important chemical groups of the active
site should lie inside of the grid box.
·
Do not make a grid box too large. A
larger grid makes the grid calculation last longer, and it takes more memory to
store the grid values in the computer's RAM. The time of the grids'
calculations is proportional to the grid box volume.
Note: If you make each side of the grid
box two times longer, then the calculation time increases 8 (2x2x2) times. The
same is true for the volume of the memory required for using grids.
·
We recommend that the grid box
volume does not exceed 20x20x20 A3. For instance, it can be 40x20x10 A3 or
5x40x40 A3 and so on.
First, select the center of the grid box by selecting any atom that lies
approximately in the middle of the active site.
After clicking, a cube with the dimensions 20x20x20 A3 will appear.
Now you have to adjust the box position and size.
·
The grid box has axes OX, OY and
OZ, which are displayed on the screen.
·
If you decide to change the size of
one of the axes, you should use Grid box Wizard (Figure 29).
Figure 29 - Grid box Wizard
·
Just click on the size button
and choose the size. The grid box will automatically be changed.
Note: The default size is 20A. The
following options are available: 5A, 10A, 15A, 20A ( default) and 25A.
Selecting Essential Metal Ions and
Hetatoms in the Active Site
BACKGROUND: The small molecule can interact with metal ions and hetatoms
in the active site. Correct energy calculation should involve all of the
important structures within the active site. After the grid box is defined, all
structures within it will be renamed (Figure 30) and shown.
Figure 30 - Active Site Structures
We have three new objects here: protein, metal and hetatom.
·
We recommend that you do not
include water molecules in modeling since Quantum has its own model of water.
You can remove any structure from the list.
Increase the grid box size to add a structure if necessary.
Adding hydrogen atoms to the protein and to the
hetatoms
·
Go to the next step - "Dock
the Molecule"- if you think the protein and all other structures in the
active site have the right number of hydrogen atoms.
· Use the Build Model option from the Wizard to set the protonation
state and add hydrogens by using Quantum's algorithms. We recommend this option.
·
Use Builder (Figure 27) to manually
set bond types and add/remove hydrogen atoms.
Figure 31 - Docking
Wizard
Choose the option regarding Protein Flexibility (Figure 31),
which is off by default.
If this option is OFF, then the protein is treated as a rigid structure.
If it is ON, then full Protein flexibility will be taken into account.
Note: Protein flexibility
capability depends on the license you purchased. This manual describes all
possible functions, and some of them may not be accessible in your
installation.
Press the Dock the Molecule button to start modeling.
Calculations and Results
All stages of the process are displayed on the Progress Bar and in the
Information Panel.
When the calculation is finished, you can see the results in a window
that will appear instead of the information panel (Figure 32).
·
E bind, kJ/mol - free binding
energy
·
E es, kJ/mol - electrostatic and
solvation energy
·
E vdw, kJ/mol - short range
electrostatic and exchange and Van der Waals energies
· TdS, kJ/mol - entropy
contribution
·
E tor, kJ/mol - ligand internal
energy change
·
Charge, Mass, Flex.bonds - total
charge, mass and number of flexible bonds of the ligand
·
RMSD, A - root mean square distance
between the initial and final positions
Note: Free binding energy is equal to
the sum of all listed contributions (E es, E vdw, TdS and E tor). In our
calculations, IC50 is 5.82 x (E bind).
Figure 32 - Results
You can compare the initial and final positions of the ligand by using
Viewer. The procedure will create the object ligand_pos with final coordinates.
You can also save the report (a) in HTML format, which is readable for
most spreadsheet applications.