We are able to screen databases of small chemical compounds to identify potential hits that could block the active site or exosite of a target protein. At present, we perform this so-called virtual screening only for protein targets and in 3D (i.e, the small molecules and the protein target are in 3D while screening when the structure of the protein target is not known is also possible).

The process is as follows:

1.  We have generated large banks of chemicals, commercially available. These small molecules were initially filtered such as to remove as much as possible compounds with undesirable elements, functional groups… 
2. The compounds, in 1D were transformed in 3D and up to 50 conformers were generated for each compound in order to allow rigid body docking… Some banks of these 3D conformations can be freely downloaded. Warning: some of these banks are over 500 Mo
3. The 3D structure of the protein target is analyzed and drugable pockets are screened. 
4. About 1 million compounds are screened per day, re-docked (the ligand is then flexible), ranked and re-ranked with different scoring functions. Such a process takes about 1-2 months or more. 
5. We propose a list of 100 to 2000 compounds, resulting from our in silico analysis, for further experimental testing. 
   

This kind of project can be performed in collaboration.
For further information, please contact: bruno.villoutreix_at_univ-paris5.fr

ADME/Tox filtering and 2D to 3D conversions were performed with Filter and Omega (http://www.eyesopen.com)