jm6b01195_si_003.pdf (1.86 MB)
Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads To Address a Catalytic Dyad
journal contribution
posted on 2016-10-11, 00:00 authored by Nedyalka Radeva, Johannes Schiebel, Xiaojie Wang, Stefan
G. Krimmer, Kan Fu, Martin Stieler, Frederik R. Ehrmann, Alexander Metz, Thomas Rickmeyer, Michael Betz, Johan Winquist, Ah Young Park, Franziska U. Huschmann, Manfred
S. Weiss, Uwe Mueller, Andreas Heine, Gerhard KlebeCrystallography is frequently used
as follow-up method to validate
hits identified by biophysical screening cascades. The capacity of
crystallography to directly screen fragment libraries is often underestimated,
due to its supposed low-throughput and need for high-quality crystals.
We applied crystallographic fragment screening to map the protein-binding
site of the aspartic protease endothiapepsin by individual soaking
experiments. Here, we report on 41 fragments binding to the catalytic
dyad and adjacent specificity pockets. The analysis identifies already
known warheads but also reveals hydrazide, pyrazole, or carboxylic
acid fragments as novel functional groups binding to the dyad. A remarkable
swapping of the S1 and S1′ pocket between structurally related
fragments is explained by either steric demand, required displacement
of a well-bound water molecule, or changes of trigonal-planar to tetrahedral
geometry of an oxygen functional group in a side chain. Some warheads
simultaneously occupying both S1 and S1′ are promising starting
points for fragment-growing strategies.