dance with aromatic atoms.

Think about new scaffold for lead generation process, a strategy is that try to replace aromatic carbon to nitrogen, oxygen, sulfur or vice varsa.

I was interested in BMS approach MORPH.
This approach was also introduced in ‘chemoinfo cook book‘.
I wrote sample code that cyclopaedically replace aromatic atoms.
The basic strategy in this code is …
1st generate all possible molecules
2nd check sanitaizemol
3rd check number of unique molecules, if number of unique molecules are not change, the program is finished.

Here is sample code…
Yesterday I wrote wrong code….

I'll revise code...

Some trials are following.
These samples are run in Ipython notebook.
And read some modules at first

from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

Screen Shot 2015-03-01 at 9.34.33 PM
Very famous molecule.
Screen Shot 2015-03-01 at 9.38.57 PM
Hmm, the code works.
Oxazole ….
Screen Shot 2015-03-01 at 9.40.23 PM
Simple example.
Screen Shot 2015-03-01 at 9.55.21 PM
OK. It’s seems to work.

One problem of this code is that to get aromatic atoms index, this code can get only Degree is lower than 3.
That’s mean this method can not replace aromatic NH, for example indole, indazole…
I will write more smart code asap.

I think to combination of some structural filter, e.g. number of nitrogen atoms in ring or lipinski, QED, Docking study etc.. is good strategy for design new molecules.


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