Molecular and Structural Characterization of Lenalidomide-Mediated Sequestration of eIF3i

Lenalidomide is a ligand of the E3
ligase substrate adapter
cereblon
(CRBN) that achieves its clinical effects in part by the promotion
of substrate recruitment and degradation. In contrast to prior targets,
eIF3i is recruited but not degraded upon complex formation with lenalidomide
and CRBN, although the structural details and mechanistic outcomes
of this interaction are unresolved. Here, we characterize the structural
basis and mechanistic outcomes of lenalidomide-induced sequestration
of eIF3i from the eIF3 complex. Identification of the binding interface
on eIF3i by a covalent lenalidomide probe and mass spectrometry rationalizes
the sequestration event. We further connect eIF3i and CRBN to lenalidomide-driven
effects on angiogenic markers, Akt1 phosphorylation, and associated
antiangiogenesis phenotypes. Finally, we find that eIF3i sequestration
is observed in MM.1S and MOLM13 cells after the degradation of other
substrates, such as IKZF1. The defined binding interface elucidated
by chemical proteomics and the observation of eIF3i sequestration
as a lenalidomide function open future directions in designing new
chemical adapters for protein sequestration as a strategy to selectively
control protein functions.