High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system

Abstract

Cereblon (CRBN) is the substrate receptor of the CRL4CRBN E3 ubiquitin ligase and is a central player in targeted protein degradation. It is the target of the thalidomide-derived immunomodulatory drugs (IMiDs) and is one of the most widely employed receptors for proteolysis-targeting chimeras (PROTACs), both of which induce the ubiquitination and subsequent proteasomal degradation of target proteins. Structural studies of ligand binding to CRBN are crucial to elucidate the mechanisms of action and for mediation of side effects, ultimately aiding the development of next-generation IMiDs and PROTACs. With this aim, a crystal-soaking system based on the single-domain bacterial homologue MsCI4 has previously been established and used to delineate the binding modes of several classes of small molecules, including FDA-approved drugs, at the molecular level. Here, this system was used to characterize the binding of the next-generation IMiDs avadomide (CC-122) and iberdomide (CC-220) at high resolution, highlighting the advantages and limitations of the MsCI4 system and its implications for the development of future cereblon effectors.

Molecular glue CELMoD compounds are regulators of cereblon conformation

“…S3C) and have high B-factors in published x-ray structures. This observation, coupled with recently described alternative positions of these extended ligand groups (14), suggests that iberdomide's interaction with the sensor loop may be dynamic. It is likely that a more stable interaction with the sensor loop could be attained with next-generation CELMoD agents.…”

“…As with pomalidomide, in the presence of excess ligand, we observe density consistent with iberdomide within the glutarimide-binding pocket of both the CRBN closed and CRBN open conformers, suggesting that drug occupancy within CRBN is not responsible for the increased allosteric transition. Two prior crystal structures of the iberdomide-bound CRBN show that the additional phenyl and morpholino moieties of the iberdomide molecule can arch over the top of the sensor loop β-hairpin ( 13 , 14 ), a conformation that may aid in the stabilization of this structural motif. These data support our proposed allosteric model whereby enhanced ligand interaction with the sensor loop stabilizes the β-hairpin conformation, which promotes the closure of the TBD and Lon domains and ultimately translates to improved neosubstrate ubiquitination and subsequent degradation efficacy.…”

Accessing three-branched high-affinity cereblon ligands for molecular glue and protein degrader design

“…CRBN E3 ligase modulators (CELMoDs), which are typically based on aminoglutarimide as the core binding moiety, [17][18][19][20][21] and to which examples such as iberdomide (CC-220, Figure 1) and mezigdomide (CC-92480) belong. 16,22,23 The structural elongation in iberdomide compared to lenalidomide enabled additional interactions with CRBN or ligase substrates leading to a more pronounced degradation of the CRBN neosubstrates, namely the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3).…”

Discovery of CRBN as a target of thalidomide: a breakthrough for progress in the development of protein degraders

“…SARs for CRBN binding have been investigated in detail by a series of studies using the thalidomide-binding domain of cereblon isoform 4 from Magnetospirillum gryphiswaldense (MsCI4). [73][74][75][76] In an early study, the uracil moiety of uridine was shown to fit in the thalidomide-binding pocket of MsCI4, albeit of lower affinity than thalidomide, suggesting that the minimal structure for CRBN binding is a cyclic imide. 73 Subsequently, detailed SARs were studied by fluorescence resonance energy transfer using MsCI4 and various cyclic imides and lactams.…”

“…2). 35,76 CC-885 is also structurally extended compared to the IMiDs class. As mentioned above, the urea moiety of CC-885 is located between E377 and H353 of CRBN and contributes to binding by hydrogen bonding to both side chains, while the methylchlorophenyl moiety is located close to GSPT1 domain 3 and probably contributes to the selective binding to GSPT1.…”