Unveiling the molecular recognition process between USP7 N-terminal TRAF-like domain and β-catenin for small molecule discovery

Protein-protein interactions drive the majority of biological processes, but their poorly characterized molecular recognition mechanism serves as bottleneck for therapeutic interventions. Recognition of substrates via specific sites induce regulation in the protein’s activity which instigates abnormalities in cellular processes. Ubiquitin specific protease-7 (USP7), a negative regulator of Wnt-signaling pathway, deubiquitinates β-catenin and causes colorectal cancer (CRC). USP7 N-terminal TRAF-like domain’s (NTLD) orthosteric site serves as hub for the recognition of substrates, however, its role for β-catenin is still elusive. Furthermore, the pivotal structural determinant and signature residues that drives recognition process between USP7 and β-catenin is unexplored. The NTLD is an unchartered territory of USP7 as no small molecules are reported by targeting its orthosteric site. Here, we underscore the key structural determinants and thermodynamic components that possibly drive the recognition of USP7-β-catenin by using extensive computational approaches. By characterizing this site, six potential hits are identified from the library of 1.1 million compounds through structure-guided virtual screening. Among six dynamically stable hits, H1 and H6 mimics the orientation and interaction map with endogenous substrate peptides at an atomic level without using any biased approach. Consequently, our approach put-forth a novel route to design potent USP7 inhibitors by targeting NTLD.