Type II Binders Targeting the “GLR-Out” Conformation of the Pseudokinase STRADα

Pseudokinases
play important roles in signal transduction and cellular
processes similar to those of catalytically competent kinases. However,
pseudokinase pharmacological tractability and conformational space
accessibility are poorly understood. Pseudokinases have only recently
been suggested to adopt “inactive” conformations or
interact with conformation-specific kinase inhibitors (e.g., type
II compounds). In this work, the heavily substituted pseudokinase
STRADα, which possesses a DFG → GLR substitution in the
catalytic site that permits nucleotide binding while impairing divalent
cation coordination, is used as a test case to demonstrate the potential
applicability of conformation-specific, type II compounds to pseudokinase
pharmacology. Integrated structural modeling is employed to generate
a “GLR-out” conformational ensemble. Likely interacting
type II compounds are identified through virtual screening against
this ensemble model. Biophysical validation of compound binding is
demonstrated through protein thermal stabilization and ATP competition.
Localization of a top-performing compound through surface methylation
strongly suggests that STRADα can adopt the “GLR-out”
conformation and interact with compounds that comply with the standard
type II pharmacophore. These results suggest that, despite a loss
of catalytic function, some pseudokinases, including STRADα,
may retain the conformational switching properties of conventional
protein kinases.