title: Effective virtual screening strategy toward covalent ligands: identification of novel NEDD8-activating enzyme inhibitors.
abstract: The NEDD8-activating enzyme (NAE) is an emerging target for cancer therapy, which regulates the degradation and turnover of a variety of cancer-related proteins by activating the cullin-RING E3 ubiquitin ligases. Among a limited number of known NAE inhibitors, the covalent inhibitors have demonstrated the most potent efficacy through their covalently linked adducts with NEDD8. Inspired by this unique mechanism, in this study, a novel combined strategy of virtual screening (VS) was adopted with the aim to identify diverse covalent inhibitors of NAE. To be specific, a docking-enabled pharmacophore model was first built from the possible active conformations of chosen covalent inhibitors. Meanwhile, a dynamic structure-based phamacophore was also established based on the snapshots derived from molecular dynamic simulation. Subsequent screening of a focused ZINC database using these pharmacophore models combined with covalent docking discovered three novel active compounds. Among them, compound LZ3 exhibited the most potent NAE inhibitory activity with an IC50 value of 1.06 ± 0.18 μM. Furthermore, a cell-based washout experiment proved the proposed covalent binding mechanism for compound LZ3, which confirmed the successful application of our combined VS strategy, indicating it may provide a viable solution to systematically discover novel covalent ligands.
authors.affiliation: State Key Laboratory of Natural Medicines, ‡Center of Drug Discovery, §Department of Pharmacology, and ∥School of Pharmacy, China Pharmaceutical University , Nanjing 210009, Jiangsu, China.
authors.forename: Shengping
authors.initials: S
authors.lastname: Zhang
authors.forename: Jiani
authors.initials: J
authors.lastname: Tan
authors.forename: Zhonghui
authors.initials: Z
authors.lastname: Lai
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.forename: Junxia
authors.initials: J
authors.lastname: Pang
authors.forename: Jianhu
authors.initials: J
authors.lastname: Xiao
authors.forename: Zhangjian
authors.initials: Z
authors.lastname: Huang
authors.forename: Yihua
authors.initials: Y
authors.lastname: Zhang
authors.forename: Hui
authors.initials: H
authors.lastname: Ji
authors.forename: Yisheng
authors.initials: Y
authors.lastname: Lai
mesh_terms: D002460:Cell Line; D062313:Databases, Pharmaceutical; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D044764:Ubiquitin-Activating Enzymes / Q000037:antagonists & inhibitors* / Q000378:metabolism
chemical_list: D004791:Enzyme Inhibitors; D008024:Ligands; D044764:Ubiquitin-Activating Enzymes; C491802:NAE protein, human