title: Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design.
abstract: Modern rational drug design not only deals with the search for ligands binding to interesting and promising validated targets but also aims to identify the function and ligands of yet uncharacterized proteins having impact on different diseases. Additionally, it contributes to the design of inhibitors with distinct selectivity patterns and the prediction of possible off-target effects. The identification of similarities between binding sites of various proteins is a useful approach to cope with those challenges. The main scope of this perspective is to describe applications of different protein binding site comparison approaches to outline their applicability and impact on molecular design. The article deals with various substantial application domains and provides some outstanding examples to show how various binding site comparison methods can be applied to promote in silico drug design workflows. In addition, we will also briefly introduce the fundamental principles of different protein binding site comparison methods.
authors.affiliation: Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, 44227 Dortmund, Germany.
authors.forename: Christiane
authors.initials: C
authors.lastname: Ehrt
authors.affiliation: Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, 44227 Dortmund, Germany.|Department of Computer Science, TU Dortmund University , Otto-Hahn-Straße 14, 44224 Dortmund, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Brinkjost
authors.affiliation: Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, 44227 Dortmund, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Koch
mesh_terms: D001665:Binding Sites; D002626:Chemistry, Pharmaceutical; D015195:Drug Design; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry
chemical_list: D011506:Proteins