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

• Published in: European journal of medicinal chemistry 2022-01, Vol.227, p.113871-113871, Article 113871
• Main Authors: Xue, Xin, Kang, Ji-Bo, Yang, Xiao, Li, Nan, Chang, Liang, Ji, Juan, Meng, Xiang-Kai, Zhang, Hai-Qing, Zhong, Yue, Yu, Shao-Peng, Wu, Wen-Yu, Wang, Xiao-Long, Li, Nian-Guang, Sun, Shan-Liang
• Format: Article
• Language: English
• Subjects: Alanine scanning; Cell Survival - drug effects; Dose-Response Relationship, Drug; Drug Design; HeLa Cells; HIF-1α/VHL; Humans; Hydroxyproline - chemical synthesis; Hydroxyproline - chemistry; Hydroxyproline - pharmacology; Hypoxia-Inducible Factor 1, alpha Subunit - antagonists & inhibitors; Hypoxia-Inducible Factor 1, alpha Subunit - metabolism; Molecular Dynamics Simulation; Molecular Structure; Protein Binding - drug effects; Protein-protein interaction; Site-directed mutagenesis; Stroke; Structure-Activity Relationship; Von Hippel-Lindau Tumor Suppressor Protein - antagonists & inhibitors; Von Hippel-Lindau Tumor Suppressor Protein - metabolism
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2021.113871

The ubiquitination of the hypoxia-inducible factor-1α (HIF-1α) 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-1α contributed the key interaction between HIF-1α 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-1α. 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-1α or HIF-1α-OH in HeLa cells. Our work provides a new orientation for the modification or design of VHL/HIF-1α protein-protein interaction inhibitors. [Display omitted] •An extra sub-pocket Site4 between H110 and Y112 was determined by virtual mutation.•8 derivates of VH032 were synthesized by introducing various groups bounded to Site4.•Inhibitory activities of all derivatives were evaluated against HIF-1α/VHL interaction.•16h displayed more potential in binding affinity, negligible cytotoxicity and stabilization of HIF-1α.