Identification of KLHL12 Ligands Using Fragment-Based Methods

Targeted protein
degradation can be induced by recruiting a protein
of interest to an E3 ligase, resulting in its ubiquitination and subsequent
proteasome-mediated degradation. However, only a small number of E3
ligases have been utilized for degradation. Expansion of the repertoire
of useful E3 ligases via the identification of ligands to those ligases
could broaden the scope and applicability of the degradation paradigm.
We have identified KLHL12 as an E3 ligase with higher expression in
cancer over normal tissues. We report here the use of NMR-based screening
to identify fragments that bind to KLHL12, and X-ray structures of
a fragment hit bound to KLHL12. Using this structural information,
we optimized the hits, leading to the first reported small molecules
that bind to KLHL12 with submicromolar affinity. Derivatives of these
compounds may be useful for the construction of PROTACs to selectively
degrade protein targets in tumors while sparing normal cells.