Q-MOL L.L.C. In Silico Pharmaceuticals

The pocket environment of a receptor can be added to the field potential, generated from a ligand, to create a pocket field potential. The pocket field potential is used for screening for potential protein targets of a given ligand, or cross-reactivity prediction. Cross-reactivity prediction is more common task, since promiscous ligands are undesirable. Although there is a limited number of compounds co-crystallized with their respective receptors, an interpolation of properties allows approximation of critical protein-ligand interactions. Thus, only few data points (co-crystal structures) are required to triangulate missing parameters. Figure 6 and Figure 7 demonstrate an application of the above ideas.

  Figure 6.    Figure 7.
The collection of pocket potentials, generated from liganded pockets from known structures, is a pocketome. The pocketome can be used not only for crossreactivity prediction but also for protein target identification of a ligand discovered, say, in cell-based high throughput screening. This technology also provides opportunity for FDA approved drug repositioning.