Development of FBXW7 binders for targeted protein degradation

Protein-protein interactions (PPIs) play essential roles in almost all the physiological processes in human cells. Inducing or enhancing the proximity of specific PPIs for targeted protein degradation (TPD) has received much attention. TPD caused by induced protein proximity is usually achieved by two categories of small molecules: molecular glues and proteolysis targeting chimeras (PROTACs). Both categories utilize the ubiquitin-mediated proteolysis system for degradation, in which E3 ligases play vital roles in substrate recognition. Despite the fact that there are over 600 E3 ligases in the human system, only less than 10% are investigated for TPD. Here we report the discovery of a set of potential binders for FBXW7, an E3 ligase and key tumor suppressor for which no previous binders have been found. Our project aims to discover potent small-molecule binders to FBXW7, which can be used as new warheads for PROTAC design for TPD and eventually suppression of various cancers. Taking advantage of our high-throughput screening technology, Small Molecule Microarrays (SMMs), we successfully identified 3 groups of compounds (44 total) that potentially bind to FBXW7 after screening our 65,000 ‘drug-like' small molecule library. This is done by printing these small molecules directly onto glass chips and incubating with in-house purified His-tag FBXW7, and then recognizing with fluorescence-conjugated antibody. We then performed secondary assays using nanoDSF, in which multiple small molecules from one of the groups induced over 0.3 ℃ change in the melting point of FBXW7, indicating binding activity. Interestingly, these small molecules share very similar chemical structures, which differ from others by merely one functional group on one of the 6-membered rings. Following thermo shift assay indicates that these small molecule candidates stabilize FBXW7 in a dose-dependent manner shown by western blot. So far, our leading compound is shown to have a binding affinity of 0.3μM to FBXW7 using ITC. Attempts to synthesize and test these binders for a set of proof-of-concept PROTACs are in progress. In summary, our findings identify a new set of potential binders to FBXW7, which expands the toolbox for PROTAC design. We also prove the strength of SMM as a viable methodology for the exploration of more E3 ligase binders, which will greatly benefit the development of tools in TPD for cancer therapeutics.