An efficient strategy for digging protein-protein interactions for rational drug design - A case study with HIF-1α/VHL

The ubiquitination of the hypoxia-inducible factor-1 alpha (HIF-1 alpha) is mediated by interacting with the von Hippel-Lindau protein (VHL), and is associated with cancer, chronic anemia, and ischemia. VHL, an E3 ligase, has been reported to degrade HIF-1 for decades, however, there are few successful inhibitors currently. Poor understanding of the binding pocket and a lack of in-depth exploration of the interactions between two proteins are the main reasons. Hence, we developed an effective strategy to identify and design new inhibitors for protein-protein interaction targets. The hydroxyproline (Hyp564) of HIF-1 alpha contributed the key interaction between HIF-1 alpha and VHL. In this study, detailed information of the binding pocket were explored by alanine scanning, site-directed mutagenesis and molecular dynamics simulations. Interestingly, we found the interaction(s) between Y565 and H110 played a key role in the binding of VHL/HIF-1 alpha. Based on the interactions, 8 derivates of VH032, 16a-h, were synthesized by introducing various groups bounded to H110. Further assay on protein and cellular level exhibited that 16a-h accessed higher binding affinity to VHL and markable or modest improvement in stabilization of HIF-1 alpha or HIF-1 alpha-OH in HeLa cells. Our work provides a new orientation for the modification or design of VHL/HIF-1 alpha protein-protein interaction inhibitors. (C) 2021 Elsevier Masson SAS. All rights reserved.

Automated summary

The study identified key interaction points between HIF-1α and VHL, and successfully synthesized a series of new inhibitors for VHL/HIF-1α protein-protein interactions. These inhibitors showed improved binding affinity and stability in cellular assays.