Selective Inhibition of hsp90 Paralogs: Uncovering the Role of Helix 1 in Grp94‐Selective Ligand Binding

ABSTRACT Grp94 is the endoplasmic reticulum paralog of the hsp90 family of chaperones, which have been targeted for therapeutic intervention via their highly conserved ATP binding sites. The design of paralog‐selective inhibitors relies on understanding the protein structural elements that drive higher affinity in selective inhibitors. Here, we determined the structures of Grp94 and Hsp90 in complex with the Grp94‐selective inhibitor PU‐H36, and of Grp94 with the non‐selective inhibitor PU‐H71. In Grp94, PU‐H36 derives its higher affinity by utilizing Site 2, a Grp94‐specific side pocket adjoining the ATP binding cavity, but in Hsp90 PU‐H36 occupies Site 1, a side pocket that is accessible in all paralogs with which it makes lower affinity interactions. The structure of Grp94 in complex with PU‐H71 shows only Site 1 binding. While changes in the conformation of helices 4 and 5 in the N‐terminal domain occur when ligands bind to Site 1 of both Hsp90 and Grp94, large conformational shifts that also involve helix 1 are associated with the engagement of the Site 2 pocket in Grp94 only. Site 2 in Hsp90 is blocked and its helix 1 conformation is insensitive to ligand binding. To understand the role of helix 1 in ligand selectivity, we tested the binding of PU‐H36 and other Grp94‐selective ligands to chimeric Grp94/Hsp90 constructs. These studies show that helix 1 is the major determinant of selectivity for Site 2 targeted ligands and also influences the rate of ATPase activity in Hsp90 paralogs.