Chemical Ligand Space of Cereblon

Abstract

The protein cereblon serves as a substrate receptor of a ubiquitin ligase complex that can be tuned toward different target proteins by cereblon-binding agents. This approach to targeted protein degradation is exploited in different clinical settings and has sparked the development of a growing number of thalidomide derivatives. Here, we probe the chemical space of cereblon binding beyond such derivatives and work out a simple set of chemical requirements, delineating the metaclass of cereblon effectors. We report co-crystal structures for a diverse set of compounds, including commonly used pharmaceuticals, but also find that already minimalistic cereblon-binding moieties might exert teratogenic effects in zebrafish. Our results may guide the design of a post-thalidomide generation of therapeutic cereblon effectors and provide a framework for the circumvention of unintended cereblon binding by negative design for future pharmaceuticals.

De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives

“…However, as the three chains form different crystal contacts and differ slightly in their conformation, it is possible that thalidomide is only replaced in one or two chains of the ASU, depending on the particular compound. 36 These experiments yielded crystal structures for the four compounds tested, 4a , 4b , 5a , and 5b , all showing the classical IMiD binding mode with the basal main-chain interactions of the succinimide amino group with F77 and the carbonyl group with W79 of MsCI4. Also, the orientation of the protruding moieties of 4a , 5a , and 5b is very similar to that of thalidomide, despite the different ring size of glutarimide and succinimide.…”

“…As a starting point for new effectors, we chose the classical IMiD scaffold. Based on the finding that succinimide is able to bind to CRBN with a higher affinity than glutarimide ( K i values of 4.3 μM vs 28 μM for MsCI4 36 ), we designed a first panel of derivatives based on glutarimide and succinimide, in which we probed the effect of different substitutions in the phthaloyl moiety (Figure 2). The respective compounds 2a–5b were prepared by the synthetic route shown in Scheme 1.…”

“…Lenalidomide ( K i = 3.1 μM) and pomalidomide ( K i = 0.8 μM), both carrying an additional amino group in the R 2 position, show improved affinity to MsCI4 as compared to thalidomide ( K i = 4.4 μM). When we exchanged this amino group for a nitro group ( 4c ), we saw a significant drop in affinity into a range in which a precise value could not be obtained ( K i > 40 μM); 36 moving this nitro group to the R 1 position ( 4d ) had less impact on the affinity ( K i = 8.9 μM, Figure 2A). Similar effects were observed in a recent study that was published during the preparation of this manuscript.…”

“…In a next step, we determined the molecular-binding determinants of the succinimide-based compounds via X-ray crystallography. To this end, crystals of the MsCI4·thalidomide complex were reproduced 36 and subsequently used for soaking experiments, in which the thalidomide molecules bound to MsCI4 may be displaced by the compound of interest. There are three chains, that is, three MsCI4·thalidomide complexes, in the asymmetric unit (ASU) of these crystals, in which the bound thalidomide molecules can potentially be displaced.…”

PROTACs– a game-changing technology

“…Thalidomide and its derivatives bind through the glutarimide ring into the aromatic cage, while the rest of the molecule protrudes from the binding pocket. More recently, Boichenko et al [58] investigated thoroughly the chemical ligand space of cereblon, by solving multiple X-ray structures. The binding of the compounds was determined by a FRET assay and teratogenic effects were evaluated in a zebrafish model.…”