title: Structural basis of RIP1 inhibition by necrostatins.
abstract: Necroptosis is a cellular mechanism that mediates necrotic cell death. The receptor-interacting serine/threonine protein kinase 1 (RIP1) is an essential upstream signaling molecule in tumor-necrosis-factor-α-induced necroptosis. Necrostatins, a series of small-molecule inhibitors, suppress necroptosis by specifically inhibiting RIP1 kinase activity. Both RIP1 structure and the mechanisms by which necrostatins inhibit RIP1 remain unknown. Here, we report the crystal structures of the RIP1 kinase domain individually bound to necrostatin-1 analog, necrostatin-3 analog, and necrostatin-4. Necrostatin, caged in a hydrophobic pocket between the N- and C-lobes of the kinase domain, stabilizes RIP1 in an inactive conformation through interactions with highly conserved amino acids in the activation loop and the surrounding structural elements. Structural comparison of RIP1 with the inhibitor-bound oncogenic kinase B-RAF reveals partially overlapping binding sites for necrostatin and for the anticancer compound PLX4032. Our study provides a structural basis for RIP1 inhibition by necrostatins and offers insights into potential structure-based drug design.
authors.affiliation: Ministry of Education Protein Science Laboratory, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Xie
authors.forename: Wei
authors.initials: W
authors.lastname: Peng
authors.forename: Yexing
authors.initials: Y
authors.lastname: Liu
authors.forename: Chuangye
authors.initials: C
authors.lastname: Yan
authors.forename: Jenny
authors.initials: J
authors.lastname: Maki
authors.forename: Alexei
authors.initials: A
authors.lastname: Degterev
authors.forename: Junying
authors.initials: J
authors.lastname: Yuan
authors.forename: Yigong
authors.initials: Y
authors.lastname: Shi
mesh_terms: D016367:Baculoviridae / Q000235:genetics; D018360:Crystallography, X-Ray; D015195:Drug Design; D006801:Humans; D007093:Imidazoles / Q000737:chemistry*; D007211:Indoles / Q000737:chemistry*; D007527:Isoenzymes / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D007700:Kinetics; D062105:Molecular Docking Simulation; D009154:Mutation; D009336:Necrosis; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D053422:Receptor-Interacting Protein Serine-Threonine Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics; D011993:Recombinant Fusion Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D007093:Imidazoles; D007211:Indoles; D007527:Isoenzymes; D011993:Recombinant Fusion Proteins; C507699:necrostatin-1; D053422:Receptor-Interacting Protein Serine-Threonine Kinases