Hot Spot Analysis of YAP-TEAD Protein-Protein Interaction Using the Fragment Molecular Orbital Method and Its Application for Inhibitor Discovery

Simple Summary YAP-TEAD protein-protein interaction is a crucial feature in the Hippo pathway for cancer therapeutics. In this study, to investigate novel YAP-TEAD protein-protein interaction inhibitors, the fragment molecular orbital method for hot spot analysis of YAP-TEAD PPI and FMO-based pharmacophore construction were introduced. We performed pharmacophore based virtual screening through an in-house library. Virtual hit compounds were derived, and the biological activity of the hit compounds was confirmed, through in vitro experiments. Finally, we proposed a compound BY03 as a novel promising PPI inhibitor for the YAP-TEAD interaction. The Hippo pathway is an important signaling pathway modulating growth control and cancer cell proliferation. Dysregulation of the Hippo pathway is a common feature of several types of cancer cells. The modulation of the interaction between yes-associated protein (YAP) and transcriptional enhancer associated domain (TEAD) in the Hippo pathway is considered an attractive target for cancer therapeutic development, although the inhibition of PPI is a challenging task. In order to investigate the hot spots of the YAP and TEAD1 interacting complex, an ab initio Fragment Molecular Orbital (FMO) method was introduced. With the hot spots, pharmacophores for the inhibitor design were constructed, then virtual screening was performed to an in-house library. Next, we performed molecular docking simulations and FMO calculations for screening results to study the binding modes and affinities between PPI inhibitors and TEAD1. As a result of the virtual screening, three compounds were selected as virtual hit compounds. In order to confirm their biological activities, cellular (luciferase activity, proximity ligation assay and wound healing assay in A375 cells, qRT-PCR in HEK 293T cells) and biophysical assays (surface plasmon resonance assays) were performed. Based on the findings of the study, we propose a novel PPI inhibitor BY03 and demonstrate a profitable strategy to analyze YAP-TEAD PPI and discover novel PPI inhibitors.