Dissecting Fragment-Based Lead Discovery at the von Hippel-Lindau Protein:Hypoxia Inducible Factor 1α Protein-Protein Interface

SummaryFragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed.

Graphical AbstractFigure optionsDownload full-size imageDownload high-quality image (182 K)Download as PowerPoint slideHighlights► Inhibitors of pVHL:HIF-1α interaction are ligand-efficient and retain binding mode ► Ro3-compliant fragments of these inhibitors are not hits in biophysical screens ► Successful hit fragments break the Ro3 and target at least two subsites at the PPI ► Integration of GE and GLE analyses provide methodology to probe hot spots at a PPI