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Is it possible to generate a structure-based pharmacophore model from the receptor binding site?

Yes. We recommend using the script E-Pharmacophores to guide the building of these types of receptor-based hypotheses. The script generates energetically optimized, structure-based pharmacophores, also known as e-pharmacophores, for use in rapid in silico screening. The method combines protein-ligand energetic terms computed by the Glide XP scoring function to rank the importance of pharmacophore features. The script is available from Maestro (Scripts → Docking Post-processing → E-Pharmacophores).

Note: To use this script, you must have a XP Visualizer license (in addition to a Glide license), and run a Glide docking job with "Write XP descriptor information" selected in the Settings tab of the Ligand Docking panel.

E-pharmacophores can be generated in cases where experimental information about ligand structure is unavailable, is not suitable for pharmacophore development (i.e., non druglike), or is at the site of a protein-protein interface; or where it is desirable to retrieve diverse compounds that are not biased by the cocrystallized ligand. However, it is possible that the best results will be obtained with an e-pharmacophore generated from docking a potent (or perhaps efficient) ligand for a given target.

There are two relevant papers describing the method and applications:

J. Chem. Inf. Model. 2009, 49, 2356–2368
J Comput. Aided Mol. Des. 2009, 23, 541–554

Keywords: receptor-based pharmacophore, Phase

Related Articles:

#214: Can I create a pharmacophore hypothesis based only on my protein binding site, without having a native ligand?

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