Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding

Grp94 and Hsp90, the ER and cytoplasmic
hsp90 paralogs, share a
conserved ATP-binding pocket that has been targeted for therapeutics.
Paralog-selective inhibitors may lead to drugs with fewer side effects.
Here, we analyzed 1 (BnIm), a benzyl imidazole resorcinylic
inhibitor, for its mode of binding. The structures of 1 bound to Hsp90 and Grp94 reveal large conformational changes in
Grp94 but not Hsp90 that expose site 2, a binding pocket adjacent
to the central ATP cavity that is ordinarily blocked. The Grp94:1 structure reveals a flipped pose of the resorcinylic scaffold
that inserts into the exposed site 2. We exploited this flipped binding
pose to develop a Grp94-selective derivative of 1. Our
structural analysis shows that the ability of the ligand to insert
its benzyl imidazole substituent into site 1, a different side pocket
off the ATP binding cavity, is the key to exposing site 2 in Grp94.