Molecular Dynamics and Drug Selection
I wanted a selection of drugs in my database, those commonly used
such as aspirin , those currently used for myeloma such as
lenalidomide, those suggested for the future for myeloma such as
JQ1, and those I feel comfortable at trying which have been taken by
humanity for centuries and derived from fruits, spices, herbs
etc. For all the drugs we need a PDB file. You might be
able to find it at the RCSB PDB site but
you will be able to do so at the Pubchem site.
Search for aspirin and you will find it , select it and the page
displays the detail with a "Download" button. Select the 2D
structure and download the SDF file. If you open it with a
text editor it displays the locations of the atoms in its
construction. If you drag it into the VegaZZ program it
displays the construction. Try "View" , "label" , "element" and you
can see the detail molecular construction. Rotating it you
will see it is a flat representation which does NOT display actual
Use edit, add, cluster, water say size 20 to "place the
molecule into water2. Then calculate , ammp, minimisation
and the molecule begins to take some shape. Save this as a PDB
( 2.2) file, say asp.pdb. If you open that file in a text
editor you can see the various atoms of its contruction with their 3
dimensional x,y,z coordinates.
Now we have a PDB file and can load it into Autodock Tools.
Here again display, label, atoms shows the
construction. This program prepares the molecule data to be
used in a docking simulation. As this is a drug it is classed
as a "ligand". So ligand, input, choose , the asp we have
loaded and charges are added, flexible bonds identified etc , ready
for docking. ligand , output , save as pdbqt gives you
the file asp.pdbqt in the location of your choice.
This needs to be done for each and every drug you wish to run test
I guess I have a hundred or so now by selection of active molecules
from turmeric, green tea, milk thistle, raspberries, apples
If you can get to the same position with curcumin then in Autodock
Tools it will look like this.