Biophysical and structural studies of the ligand-induced interaction of multiple SALL4 zinc finger domains with cereblon

Although several proteins are known to interact with cereblon in the presence of molecular glues (MGs), the molecular basis of selectivity is emerging. An understanding of these interactions is important when designing drugs that selectively degrade a given target while sparing others. SALL4 degradation is undesirable and X-ray crystallography and biophysical binding studies expand our understanding of the minimal binding domain recognized by cereblon in the presence of IMiDs pomalidomide and CC-220. Structures of a complex of DDB1:CRBN in the presence of these IMiDs with SALL4 zinc finger domains reveal a novel binding mode involving two adjacent zinc fingers- a primary and a secondary zinc finger. The primary interactions occur between the C-terminal domain IMiD-binding domain of cereblon and SALL4 ZF2, which contains the canonical CXXCG motif that is known to interact with cereblon:pomalidomide complexes. In addition, adjacent SALL4 ZF1 binds to the N-terminal domain of cereblon in the “closed” form. The binding affinities of the single and double zinc finger domains of cereblon are consistent with these structural elements. Adding C-terminal residues to ZF2 results in increased potency due to additional contacts with cereblon. With respect to selectivity, the binding of ZF2 or ZF1-2 domains to the CRBN:CC-220 complex is weaker than the corresponding pomalidomide complexes and structural studies suggest subtle structural changes in cereblon and SALL4 ZF1 that do not occur in the corresponding pomalidomide. These studies further our understanding of the molecular glue-mediated interactions of zinc finger-based proteins with cereblon and may provide structural tools for the prospective design of compounds with reduced binding and degradation of SALL4