Structural basis for Cullins and RING component inhibition: Targeting E3 ubiquitin pathway conductors for cancer therapeutics

Abstract

Cullin (CUL)-RING E3 ubiquitin ligases (CRLs) are attractive therapeutic targets as they regulate diverse biological processes important for cancer cell survival by conferring substrate selectivity for ubiquitination and degradation. Given the complexity of CRL complexes, steps toward the structure-based design of small-molecule inhibitors to modulate their activity have remained elusive. In this study, we explored the structural assembly and interaction details of closely related CUL scaffolds (CUL1, CUL2, CUL3, CUL4A, CUL4B, CUL5 and CUL7) with RBX1 to screen potent small molecules against CRLs. The RING-Box (RBX1 and RBX2) proteins heterodimerize with CULs and dynamically facilitate the ubiquitination process. The docked complexes of conserved CUL C-terminal domains exhibited a common RBX1 binding pattern through the incorporation of intermolecular β-sheet and α/β core, stabilized by hydrophobic contacts. The comparative binding pattern analysis of CUL-RBX1 interfaces revealed a unique structural motif (VLYRLWLN) that directs the binding of RBX1 N-terminal β-strand. Through reinvigorating the subtle structural dynamics of bound complexes and application of structure-based drug design approaches, we proposed a set of inhibitors which could be further optimized to target CRL activity. One reference compound (C64) was extensively characterized for selective binding at the RBX1-binding grooves/VLYRLWLN of CUL1-7. We speculate that mechanistic information of the individual residual contributions through structure-guided approaches could be pivotal for the rational design of more promising and active drug candidates against CRLs.