TY - JOUR

T1 - Development of Noncovalent Small-Molecule Keap1-Nrf2 Inhibitors by Fragment-Based Drug Discovery

AU - Narayanan, Dilip

AU - Tran, Kim T

AU - Pallesen, Jakob S

AU - Solbak, Sara M Ø

AU - Qin, Yuting

AU - Mukminova, Elina

AU - Luchini, Martina

AU - Vasilyeva, Kristina O

AU - González Chichón, Dorleta

AU - Goutsiou, Georgia

AU - Poulsen, Cecilie

AU - Haapanen, Nanna

AU - Popowicz, Grzegorz M

AU - Sattler, Michael

AU - Olagnier, David

AU - Gajhede, Michael

AU - Bach, Anders

N1 - Funding Information: This research was supported by the Lundbeck Foundation (grant R190-2014-3710 for A.B.); the A. P. Møller Foundation for the Advancement of Medical Science (grant 14-28 for A.B.); the Hørslev Foundation (grant 203866-MIA for A.B.); the Augustinus Foundation (grant 14-1571 for A.B.); the Drug Research Academy/Lundbeck Foundation (scholarship for K.T.T.); and the China Scholarship Council (file no. 202009370089 to Y.Q.). We also acknowledge funding from the European Union’s Framework Programme for Research and Innovation Horizon 2020 (2014-2020) under the Marie Skłodowska-Curie Grant Agreement No. 675555, Accelerated Early staGe drug discovery (AEGIS); and the Helmholtz Center Munich to M.S. and G.P.; and access to NMR measurements at the Bavarian NMR Center and at University of Copenhagen (the latter supported by grant no. 10-085264 from The Danish Research Council for Independent Research|Nature and Universe and grant R77-A6742 from the Lundbeck Foundation). We thank all the staff at the European beamlines (ID29 and ID23-1 at ESRF, France; P13 and P14 at DESY, Germany; and BioMAX at MAX IV, Sweden) for beamtime and their support. D.O. was supported by the Lundbeck Foundation (R335-2019-2138), the Danish Cancer Society (R279-A16218), the Brødrene Hartmanns Fond, the Hørslev Foundation, the fabrikant Einar Willumsens mindelegat, the Eva og Henry Frænkels Mindefond, and the Th. Maigaards eftf. fru Lily Benthine Lunds Fond af 1.6.1978. The authors also would like to thank Laureano de la Vega (Dundee University, Scotland) for kindly sharing his NRF2 KO HaCaT cells. Publisher Copyright: © 2022 American Chemical Society.

PY - 2022

Y1 - 2022

N2 - Targeting the protein-protein interaction (PPI) between the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) and its repressor, Kelch-like ECH-associated protein 1 (Keap1), constitutes a promising strategy for treating diseases involving oxidative stress and inflammation. Here, a fragment-based drug discovery (FBDD) campaign resulted in novel, high-affinity (Ki = 280 nM), and cell-active noncovalent small-molecule Keap1-Nrf2 PPI inhibitors. We screened 2500 fragments using orthogonal assays-fluorescence polarization (FP), thermal shift assay (TSA), and surface plasmon resonance (SPR)-and validated the hits by saturation transfer difference (STD) NMR, leading to 28 high-priority hits. Thirteen co-structures showed fragments binding mainly in the P4 and P5 subpockets of Keap1's Kelch domain, and three fluorenone-based fragments featuring a novel binding mode were optimized by structure-based drug discovery. We thereby disclose several fragment hits, including their binding modes, and show how FBDD can be performed to find new small-molecule Keap1-Nrf2 PPI inhibitors.

AB - Targeting the protein-protein interaction (PPI) between the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) and its repressor, Kelch-like ECH-associated protein 1 (Keap1), constitutes a promising strategy for treating diseases involving oxidative stress and inflammation. Here, a fragment-based drug discovery (FBDD) campaign resulted in novel, high-affinity (Ki = 280 nM), and cell-active noncovalent small-molecule Keap1-Nrf2 PPI inhibitors. We screened 2500 fragments using orthogonal assays-fluorescence polarization (FP), thermal shift assay (TSA), and surface plasmon resonance (SPR)-and validated the hits by saturation transfer difference (STD) NMR, leading to 28 high-priority hits. Thirteen co-structures showed fragments binding mainly in the P4 and P5 subpockets of Keap1's Kelch domain, and three fluorenone-based fragments featuring a novel binding mode were optimized by structure-based drug discovery. We thereby disclose several fragment hits, including their binding modes, and show how FBDD can be performed to find new small-molecule Keap1-Nrf2 PPI inhibitors.

KW - PROTEIN-PROTEIN INTERACTION

KW - MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE

KW - KINETIC/AFFINITY INTERACTION CONSTANTS

KW - FLUORESCENCE POLARIZATION

KW - OXIDATIVE STRESS

KW - DIFFUSION-COEFFICIENTS

KW - COMPOUND INTERFERENCE

KW - NRF2 ACTIVATORS

KW - AMINO ESTERS

KW - BINDING

U2 - 10.1021/acs.jmedchem.2c00830

DO - 10.1021/acs.jmedchem.2c00830

M3 - Journal article

C2 - 36263945

VL - 65

SP - 14481

EP - 14526

JO - Journal of Medicinal Chemistry

JF - Journal of Medicinal Chemistry

SN - 0022-2623

IS - 21

ER -