Pharmacophore Modeling

Pharmacophore approaches are successful subfields of computer-aided drug design (CADD) which have become one of the major tools in hit identification, lead optimization, and rational design of novel drugs. A pharmacophore model is the ensemble of common steric and electronic features that are necessary to ensure the optimal molecular interactions with a specific biological target and to trigger (or block) its biological response. It can be used to represent and characterize molecules on schematic 2D or 3D level by identifying the essential properties of molecular recognition. Every type of atom or group in a compound can be reduced to a pharmacophore feature (or pharmacophore fingerprints). These molecular patterns would be labeled by several chemical properties, such as hydrogen bond donors or acceptors, aromatic, cationic, etc, which can be used to analyze the similarity among a library of small molecules and identify the key contributing features to the biological function.

Profacgen takes advantage of the most state-of-the-art techniques and software tools for pharmacophore modeling. Depending on the situation and the type of experiment, multiple strategies are available to construct pharmacophore models either in a ligand-based manner, or in a structure-based manner.

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