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将非共价 Kelch 样 ECH 相关蛋白 1(Keap1)抑制剂解构为片段,以构建新的有效化合物。

Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds.

机构信息

Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.

Food and Drug Department, University of Parma, Parco Area delle Scienze 27/a, 43124 Parma, Italy.

出版信息

J Med Chem. 2021 Apr 22;64(8):4623-4661. doi: 10.1021/acs.jmedchem.0c02094. Epub 2021 Apr 5.

Abstract

Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in a fragment-based deconstruction reconstruction (FBDR) study and tested in four orthogonal assays. This gave 17 fragment hits of which six were shown by X-ray crystallography to bind in the Keap1 Kelch binding pocket. Two hits were merged into compound with a 220-380-fold stronger affinity ( = 16 μM) relative to the parent fragments. Systematic optimization resulted in several novel analogues with values of 0.04-0.5 μM, binding modes determined by X-ray crystallography, and enhanced microsomal stability. This demonstrates how FBDR can be used to find new fragment hits, elucidate important ligand-protein interactions, and identify new potent inhibitors of the Keap1-Nrf2 PPI.

摘要

靶向核因子红细胞 2 相关因子 2(Nrf2)和 Kelch 样 ECH 相关蛋白 1(Keap1)之间的蛋白-蛋白相互作用(PPI)是控制涉及氧化应激的疾病的潜在治疗策略。在这里,将六种已知的小分子 Keap1-Nrf2 PPI 抑制剂在基于片段的解构重建(FBDR)研究中分解为 77 个片段,并在四个正交测定中进行了测试。这得到了 17 个片段命中物,其中 6 个通过 X 射线晶体学显示与 Keap1 Kelch 结合口袋结合。两个命中物融合成化合物 ,与亲本片段相比,亲和力增强了 220-380 倍( = 16 μM)。系统优化得到了几个新型类似物, 值为 0.04-0.5 μM,通过 X 射线晶体学确定了结合模式,并提高了微粒体稳定性。这证明了 FBDR 如何用于发现新的片段命中物,阐明重要的配体-蛋白相互作用,并鉴定 Keap1-Nrf2 PPI 的新有效抑制剂。

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