Fragment‐Based Drug Discovery of Novel High‐affinity, Selective, and Anti‐inflammatory Inhibitors of the Keap1‐Nrf2 Protein‐Protein Interaction
Abstract
Abstract Activating the cytoprotective response of nuclear factor erythroid 2‐related factor 2 (Nrf2) can reduce oxidative stress and inflammation. A promising strategy is to inhibit the protein‐protein interaction between Kelch‐like ECH‐associated protein 1 (Keap1) and Nrf2 using noncovalent compounds that target the Keap1 Kelch domain. These compounds may be more specific than covalent Keap1‐reacting Nrf2 activators. However, the development of drug‐like noncovalent Keap1‐Nrf2 inhibitors faces challenges due to the size and polarity of the Kelch binding pocket. Here, we present a new series of noncovalent Keap1‐Nrf2 inhibitors developed from a weak fragment hit identified by crystallographic screening. A two‐step growing strategy and optimization guided by several X‐ray cocrystal structures led to compounds with low nanomolar affinities and complete selectivity for Keap1 in a panel of homologous Kelch domains. In cells, compounds 24 and 28 potently activated the expression of Nrf2‐controlled genes and showed anti‐inflammatory effects by downregulating NLRP3 inflammasome and STING signalling activation. RNA sequencing revealed activation of cytoprotective pathways and a different profile from typical covalent Nrf2 activators. This work highlights the potential of fragment‐based drug discovery for challenging targets like Keap1 and introduces novel Keap1‐Nrf2 inhibitors as chemical probes and drug leads.
Article Details
Authors (24)
Chunyu Lin
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark
Dilip Narayanan
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark
Marilia Barreca
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark
Cecilie Poulsen
Department of Biomedicine Faculty of Health Aarhus University Aarhus 8000 Denmark
Leandro Silva da Costa
Department of Biomedicine Faculty of Health Aarhus University Aarhus 8000 Denmark
Xiangrong Chen
Kendall G. Wichman
Department of Biology Fort Lewis College Durango Colorado 81301 USA
Cherisse A. Charley
Department of Biology Fort Lewis College Durango Colorado 81301 USA
Jaslin L. Lindsay
Department of Biology Fort Lewis College Durango Colorado 81301 USA
Mahya Dezfouli
Assays Profiling and Cell Sciences, Discovery Sciences Biopharmaceuticals R&D AstraZeneca Gothenburg Sweden
Dimitra Vlissari
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark
Thomas S. Mortensen
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark
Camilla B. Chan
Jingyi Wang
William Richardson
Charlotte E. Manning
Centre for Medicines Discovery, Nuffield Department of Medicine University of Oxford Oxford OX3 7FZ UK
Zhuoyao Chen
Jie Zang
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark
Helena Käck
Protein Sciences, Structure and Biophysics, Discovery Sciences Biopharmaceuticals R&D AstraZeneca Gothenburg Sweden
Michael Gajhede
Alex N. Bullock
David J. Blake
Department of Biology Fort Lewis College Durango Colorado 81301 USA
David Olagnier
Department of Biomedicine Faculty of Health Aarhus University Aarhus 8000 Denmark
Anders Bach
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences University of Copenhagen Copenhagen 2100 Denmark