Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme

Structure. 2017 Jul 5;25(7):1120-1129.e3. doi: 10.1016/j.str.2017.05.001. Epub 2017 Jun 1.

Abstract

Targeting the activating enzymes (E1) of ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) has emerged as a promising anti-cancer strategy, possibly overcoming the ineffectiveness of proteasome inhibitors against solid tumors. Here, we report crystal structures of the yeast ubiquitin E1 (Uba1) with three adenosyl sulfamate inhibitors exhibiting different E1 specificities, which are all covalently linked to ubiquitin. The structures illustrate how the chemically diverse inhibitors are accommodated within the adenylation active site. When compared with the previously reported structures of various E1 enzymes, our structures provide the basis of the preferences of these inhibitors for different Ub/Ubl-activating enzymes. In vitro inhibition assays and molecular dynamics simulations validated the specificities of the inhibitors as deduced from the structures. Taken together, the structures establish a framework for the development of additional compounds targeting E1 enzymes, which will display higher potency and selectivity.

Keywords: E1 enzymes; adenosyl sulfamate inhibitors; cancer; drug design; ubiquitin; ubiquitin-activating enzyme; ubiquitin-like protein.

MeSH terms

  • Binding Sites
  • Cyclopentanes / pharmacology*
  • Enzyme Inhibitors / pharmacology*
  • Humans
  • Mutation
  • Nucleosides / pharmacology*
  • Protein Binding
  • Pyrimidines / pharmacology*
  • Quantitative Structure-Activity Relationship
  • Saccharomyces cerevisiae Proteins / antagonists & inhibitors
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Substrate Specificity
  • Sulfonamides / pharmacology*
  • Ubiquitin-Activating Enzymes / antagonists & inhibitors
  • Ubiquitin-Activating Enzymes / chemistry*
  • Ubiquitin-Activating Enzymes / genetics
  • Ubiquitin-Activating Enzymes / metabolism

Substances

  • Cyclopentanes
  • Enzyme Inhibitors
  • MLN7243
  • Nucleosides
  • Pyrimidines
  • Saccharomyces cerevisiae Proteins
  • Sulfonamides
  • UBE1 protein, human
  • Ubiquitin-Activating Enzymes
  • pevonedistat