title: Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
abstract: Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small-molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X-ray crystallographic screen was used to identify two distinct small-molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9-5.8 mm. Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand-induced rigidification of Ubc9 as a mechanism of inhibition.
authors.affiliation: Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: William M
authors.initials: WM
authors.lastname: Hewitt
authors.affiliation: Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.|Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
authors.forename: George T
authors.initials: GT
authors.lastname: Lountos
authors.affiliation: Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Katherine
authors.initials: K
authors.lastname: Zlotkowski
authors.affiliation: Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Samuel D
authors.initials: SD
authors.lastname: Dahlhauser
authors.affiliation: Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Lindsey B
authors.initials: LB
authors.lastname: Saunders
authors.affiliation: Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Needle
authors.affiliation: Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Joseph E
authors.initials: JE
authors.lastname: Tropea
authors.affiliation: State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) and Department of Physics, Fudan University, Shanghai, P.R. China.
authors.forename: Chendi
authors.initials: C
authors.lastname: Zhan
authors.affiliation: State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE) and Department of Physics, Fudan University, Shanghai, P.R. China.
authors.forename: Guanghong
authors.identifier: 0000-0001-5814-3328
authors.initials: G
authors.lastname: Wei
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Buyong
authors.identifier: 0000-0002-7383-719X
authors.initials: B
authors.lastname: Ma
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA.|Department of Human Genetics and Molecular Medicine, Tel Aviv University, Sackler School of Medicine, Tel Aviv, 69978, Israel.
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.affiliation: Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: David S
authors.identifier: 0000-0003-0776-8488
authors.initials: DS
authors.lastname: Waugh
authors.affiliation: Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA. schneeklothjs@mail.nih.gov.
authors.forename: John S
authors.identifier: 0000-0001-7459-783X
authors.initials: JS
authors.lastname: Schneekloth
mesh_terms: D000494:Allosteric Regulation; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006801:Humans; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D054852:Small Molecule Libraries / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D058207:Sumoylation; D020349:Surface Plasmon Resonance; D044763:Ubiquitin-Conjugating Enzymes / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D000098843:Ubiquitin-Conjugating Enzyme UBC9
chemical_list: D008024:Ligands; D054852:Small Molecule Libraries; D044763:Ubiquitin-Conjugating Enzymes; D000098843:Ubiquitin-Conjugating Enzyme UBC9
keywords: SUMOylation; Ubc9; X-ray crystallography; allostery; inhibitors