Structural basis of N-Myc binding by Aurora-A and its destabilization by kinase inhibitors

Abstract

Myc family proteins promote cancer by inducing widespread changes in gene expression. Their rapid turnover by the ubiquitin–proteasome pathway is regulated through phosphorylation of Myc Box I and ubiquitination by the E3 ubiquitin ligase SCFFbxW7. However, N-Myc protein (the product of theMYCNoncogene) is stabilized in neuroblastoma by the protein kinase Aurora-A in a manner that is sensitive to certain Aurora-A–selective inhibitors. Here we identify a direct interaction between the catalytic domain of Aurora-A and a site flanking Myc Box I that also binds SCFFbxW7. We determined the crystal structure of the complex between Aurora-A and this region of N-Myc to 1.72-Å resolution. The structure indicates that the conformation of Aurora-A induced by compounds such as alisertib and CD532 is not compatible with the binding of N-Myc, explaining the activity of these compounds in neuroblastoma cells and providing a rational basis for the design of cancer therapeutics optimized for destabilization of the complex. We also propose a model for the stabilization mechanism in which binding to Aurora-A alters how N-Myc interacts with SCFFbxW7to disfavor the generation of Lys48-linked polyubiquitin chains.

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma

“…FBXW7 encodes a member of the F box protein family and is frequently deleted/mutated in cancer, supporting its tumor-suppressive function (Davis et al., 2014); notably in relation to H3.3G34R/V it has been reported to play a role in MYC/MYCN stabilization through its action as a component of the SCF-like ubiquitin ligase complex that targets MYC/MYCN for proteasomal degradation (Welcker et al., 2004, Yada et al., 2004). With MYCN upregulated in H3.3G34R/V tumors through differential H3K36me3 binding (Bjerke et al., 2013), this observation adds to the mechanisms by which Myc proteins exert their influence in this subgroup, and provide further rationale for the observed effects of disrupting these interactions, such as with Aurora kinase A inhibitors which target the direct interaction between the catalytic domain of Aurora A and a site flanking Myc Box I that also binds SCF/FbxW7 (Richards et al., 2016). …”

Drugging the 'undruggable' cancer targets

“…No crystal structure of the complex between AURKA and MYCN was known when we reported the first amphosteric MYC inhibitor, making further optimization somewhat challenging. Fortunately, Richard Bayliss’s lab recently revealed the co-complex of AURKA bound to MYCN, which will greatly facilitate further chemical optimization of this strategy for drugging MYC 16 . As MYC is often overexpressed in late-stage cancer, targeting it for degradation is an attractive strategy in many settings.…”

The Expanding World of N-MYC–Driven Tumors

“…N-MYC is stabilized in human tumor cells and in mouse models of neuroblastoma, medulloblastoma, and NEPC by association with the Aurora-A kinase. Aurora-A binds N-MYC at residues 28-89 in N-MYC via two interaction surfaces that flank MYCBoxI, which contains the phosphodegron recognized by FBXW7 (146). FBXW7, in addition to binding to the phosphodegron, interacts with residues 62-89 of N-MYC.…”