Virtual screening of 3-(1H-1,2,3-triazol-1-yl)piperidine-2,6-dione-based compounds as new potential Cereblon modulators amenable for targeted protein degradation

Cereblon (CRBN) is a ubiquitin ligase E3 substrate receptor protein that facilitates the transfer of ubiquitin to a protein of interest (POI) through reversible interactions with the CRL4 core complex, which consists of the Cullin-4 scaffold, the DNA damage-binding protein 1 (DDB1) adaptor protein, and RING finger protein ROC1. Due to its pivotal role in protein ubiquitination, CRBN is commonly targeted for triggering the degradation of a POI. Several modulators (e.g., thalidomide, pomalidomide, lenalidomide) were identified as able to enhance the transition from an open to a closed conformation of CRBN and they act as molecular glues, thereby facilitating the recruitment and subsequentdegradation of the POIs (e.g., IKZF1, IKZF2, CK1, GSPT1) . Also, they are used as E3 ligands in the design of novel Proteolysis Targeting Chimeras (PROTACs) heterobifunctional molecules. However, CRBN modulators are often unstable and easily undergo hydrolysis in body fluids2 and, accordingly, the identification of novel molecules is urgently needed. To identify novel CRBN binders with improved chemical stability, we generated a virtual library of 3-(1H-1,2,3-triazol-1-yl)piperidine-2,6-dione-based compounds: 1838 commercially available terminal alkynes were combined with 3-azido-2,6-piperidinedione for producing a final set of 1838 compounds (CombiGlide software), whose pharmacokinetic properties were subsequently predicted (QikProp software). The filtered library with a favorable ADME profile was used as input for a molecular docking-based virtual screening campaign on CRBN. The analysis of docking scores and interactions with CRBN key amino acids led to the selection of 12 new items for the next stages of chemical synthesis and biophysical/biological evaluation, which is ongoing. In the future, we plan to replace the E3 ligase molecular portion of known PROTACs with the new identified CRBN modulators, with the final aim of improving pharmacokinetic properties and degradation efficiency of these heterobifunctional molecules.