title: Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study.
abstract: Fragment-based lead discovery (FBLD) has become a pillar in drug development. Typical applications of this method comprise at least two biophysical screens as prefilter and a follow-up crystallographic experiment on a subset of fragments. Clearly, structural information is pivotal in FBLD, but a key question is whether such a screening cascade strategy will retrieve the majority of fragment-bound structures. We therefore set out to screen 361 fragments for binding to endothiapepsin, a representative of the challenging group of aspartic proteases, employing six screening techniques and crystallography in parallel. Crystallography resulted in the very high number of 71 structures. Yet alarmingly, 44% of these hits were not detected by any biophysical screening approach. Moreover, any screening cascade, building on the results from two or more screening methods, would have failed to predict at least 73% of these hits. We thus conclude that, at least in the present case, the frequently applied biophysical prescreening filters deteriorate the number of possible X-ray hits while only the immediate use of crystallography enables exhaustive retrieval of a maximum of fragment structures, which represent a rich source guiding hit-to-lead-to-drug evolution.
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Schiebel
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Nedyalka
authors.initials: N
authors.lastname: Radeva
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Stefan G
authors.initials: SG
authors.lastname: Krimmer
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Stieler
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Frederik R
authors.initials: FR
authors.lastname: Ehrmann
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Kan
authors.initials: K
authors.lastname: Fu
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Metz
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.|Helmholtz-Zentrum Berlin für Materialien und Energie, HZB , BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
authors.forename: Franziska U
authors.initials: FU
authors.lastname: Huschmann
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie, HZB , BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
authors.forename: Manfred S
authors.initials: MS
authors.lastname: Weiss
authors.affiliation: Helmholtz-Zentrum Berlin für Materialien und Energie, HZB , BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Mueller
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Heine
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität 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 / Q000737:chemistry; D001703:Biophysics; D002151:Calorimetry; D018360:Crystallography, X-Ray; D062126:Databases, Chemical; D055808:Drug Discovery / Q000379:methods*; D008958:Models, Molecular; D011480:Protease Inhibitors / Q000737:chemistry; D011485:Protein Binding; D013329:Structure-Activity Relationship
chemical_list: D011480:Protease Inhibitors; D016282:Aspartic Acid Endopeptidases; C042466:Endothia aspartic proteinase