Drug Design-Experimental (PHC543)
Drug Design
Lab Manual
(PHC543)
Fourth Year
Students
1|Page
,Introduction to the Discovery Studio software environment
Menus
Sketching toolbar
Discovery Studio Interface
3D molecule window
Explorers
s
Hierarchy
2|Page
,Exploring the toolbar buttons and mouse:
Click each of the following buttons on the View toolbar in turn and drag the cursor
around in the Graphics View of the 3D window:
Select: Allows you to select items in the 3D Window. Select a region of the
protein in the Graphics View by clicking and dragging the lasso around a portion
of the structure. You can add to the current selection by pressing SHIFT and
encircling another region with the lasso.
Rotate: Allows you to rotate the view of the structure in the Graphics View.
Press SHIFT when rotating to rotate about the Z-axis. Rotation can also be
performed while in translation or zoom mode by clicking and holding the right-
mouse button and dragging the cursor.
Translate: Allows you to translate the structure in the Graphics View of the
3D Window. Clicking and dragging translates the molecule in the XY plane, while
pressing SHIFT and dragging the cursor translates the protein along the Z-axis.
Zoom: Allows you to enlarge or reduce the view of the structure. Zoom in by
dragging the cursor upward. Dragging the cursor downward zooms out. Click the
Zoom tool button on the View toolbar to enter zoom mode. Drag the cursor up and
down in the Graphics View of the 3D Window to zoom in and out of the molecule.
If the Hierarchy View is not visible, press CTRL+H make it visible or,
alternatively, choose Hierarchy from the View menu of the menu toolbar.
Deselect current selection by clicking another object to make a new selection, or
click in a blank area in the Graphics View of the 3D Window to deselect
everything.
3|Page
, Case Study 1:
Introduction to Discovery Studio sketching and chemistry toolbar: building
and editing Diazepam
Purpose: Introducing the sketching tools
Modules: Discovery Studio Visualizer
Introduction:
In this lesson, you will construct a small molecule using a variety of tools from the
sketching and chemistry toolbars. The molecule you will build is the 1,4-
benzodiazepine drug, Diazepam (Valium®)
Molecular structure of diazepam (7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-
benzodiazepin-2-one)
O
1N 2
3
7
Cl N
6 5 4
This tutorial covers:
1. Opening a new 3D window
2. Building the six-membered aromatic ring of the fused ring system.
3. Building the seven-membered ring
4. Adding the side chains
5. Changing element types
6. Adding the carbonyl group
7. Adding the final double bond
8. Adding hydrogen atoms and cleaning the structure.
4|Page
Drug Design
Lab Manual
(PHC543)
Fourth Year
Students
1|Page
,Introduction to the Discovery Studio software environment
Menus
Sketching toolbar
Discovery Studio Interface
3D molecule window
Explorers
s
Hierarchy
2|Page
,Exploring the toolbar buttons and mouse:
Click each of the following buttons on the View toolbar in turn and drag the cursor
around in the Graphics View of the 3D window:
Select: Allows you to select items in the 3D Window. Select a region of the
protein in the Graphics View by clicking and dragging the lasso around a portion
of the structure. You can add to the current selection by pressing SHIFT and
encircling another region with the lasso.
Rotate: Allows you to rotate the view of the structure in the Graphics View.
Press SHIFT when rotating to rotate about the Z-axis. Rotation can also be
performed while in translation or zoom mode by clicking and holding the right-
mouse button and dragging the cursor.
Translate: Allows you to translate the structure in the Graphics View of the
3D Window. Clicking and dragging translates the molecule in the XY plane, while
pressing SHIFT and dragging the cursor translates the protein along the Z-axis.
Zoom: Allows you to enlarge or reduce the view of the structure. Zoom in by
dragging the cursor upward. Dragging the cursor downward zooms out. Click the
Zoom tool button on the View toolbar to enter zoom mode. Drag the cursor up and
down in the Graphics View of the 3D Window to zoom in and out of the molecule.
If the Hierarchy View is not visible, press CTRL+H make it visible or,
alternatively, choose Hierarchy from the View menu of the menu toolbar.
Deselect current selection by clicking another object to make a new selection, or
click in a blank area in the Graphics View of the 3D Window to deselect
everything.
3|Page
, Case Study 1:
Introduction to Discovery Studio sketching and chemistry toolbar: building
and editing Diazepam
Purpose: Introducing the sketching tools
Modules: Discovery Studio Visualizer
Introduction:
In this lesson, you will construct a small molecule using a variety of tools from the
sketching and chemistry toolbars. The molecule you will build is the 1,4-
benzodiazepine drug, Diazepam (Valium®)
Molecular structure of diazepam (7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-
benzodiazepin-2-one)
O
1N 2
3
7
Cl N
6 5 4
This tutorial covers:
1. Opening a new 3D window
2. Building the six-membered aromatic ring of the fused ring system.
3. Building the seven-membered ring
4. Adding the side chains
5. Changing element types
6. Adding the carbonyl group
7. Adding the final double bond
8. Adding hydrogen atoms and cleaning the structure.
4|Page
