title: Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin.
abstract: Successful optimization of a given lead scaffold requires thorough binding-site mapping of the target protein particular in regions remote from the catalytic center where high conservation across protein families is given. We screened a 361-entry fragment library for binding to the aspartic protease endothiapepsin by crystallography. This enzyme is frequently used as a surrogate for the design of renin and β-secretase inhibitors. A hit rate of 20% was achieved, providing 71 crystal structures. Here, we discuss 45 binding poses of fragments accommodated in pockets remote from the catalytic dyad. Three major hot spots are discovered in remote binding areas: Asp81, Asp119, and Phe291. Compared to the dyad binders, bulkier fragments occupy these regions. Many of the discovered fragments suggest an optimization concept on how to grow them into larger ligands occupying adjacent binding pockets that will possibly endow them with the desired selectivity for one given member of a protein family.
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Nedyalka
authors.initials: N
authors.lastname: Radeva
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Stefan G
authors.initials: SG
authors.lastname: Krimmer
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Stieler
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Kan
authors.initials: K
authors.lastname: Fu
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Frederik R
authors.initials: FR
authors.lastname: Ehrmann
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Metz
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.|Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II , Albert-Einstein-Straße 15, 12489 Berlin, Germany.
authors.forename: Franziska U
authors.initials: FU
authors.lastname: Huschmann
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II , Albert-Einstein-Straße 15, 12489 Berlin, Germany.
authors.forename: Manfred S
authors.initials: MS
authors.lastname: Weiss
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II , Albert-Einstein-Straße 15, 12489 Berlin, Germany.|MAX IV Laboratory, Lund University , Fotongatan 2, 225 94 Lund, Sweden.
authors.forename: Uwe
authors.initials: U
authors.lastname: Mueller
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Schiebel
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Heine
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Klebe
mesh_terms: D016282:Aspartic Acid Endopeptidases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D055162:Biocatalysis; D020134:Catalytic Domain / Q000187:drug effects; D018360:Crystallography, X-Ray; D008024:Ligands; D008958:Models, Molecular; D011480:Protease Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D011480:Protease Inhibitors; D016282:Aspartic Acid Endopeptidases; C042466:Endothia aspartic proteinase