Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1–Nrf2 Protein–Protein Interaction

Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning

(2021) Paula C. Ortet et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2021) Jakob S. Pallesen et al.   JOURNAL OF MEDICINAL CHEMISTRY

A practical guide to large-scale docking

(2021) Brian J. Bender et al.   Nature Protocols

Solution conformations explain the chameleonic behaviour of macrocyclic drugs

(2020) Emma Danelius et al.   CHEMISTRY-A EUROPEAN JOURNAL

A Fully Integrated Assay Panel for Early Drug Metabolism and Pharmacokinetics Profiling

(2020) Johan Wernevik et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Generating multibillion chemical space of readily accessible screening compounds

(2020) Oleksandr O. Grygorenko et al.   iScience

Mining Natural Products for Macrocycles to Drug Difficult Targets

(2020) Fabio Begnini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting the Permeability of Macrocycles from Conformational Sampling – Limitations of Molecular Flexibility

(2020) Vasanthanathan Poongavanam et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases

(2019) Antonio Cuadrado et al.   NATURE REVIEWS DRUG DISCOVERY

A Comparative Assessment Study of Known Small-Molecule Keap1−Nrf2 Protein–Protein Interaction Inhibitors: Chemical Synthesis, Binding Properties, and Cellular Activity

(2019) Kim T. Tran et al.   JOURNAL OF MEDICINAL CHEMISTRY

A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1–12): Synthesis and NMR Ensemble Analysis of Nisin(1–12) and Analogues

(2019) Rachael Dickman et al.   CHEMISTRY-A EUROPEAN JOURNAL

Interaction Energetics and Druggability of the Protein–Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

(2019) Mengqi Zhong et al.   BIOCHEMISTRY

Design, synthesis and identification of novel, orally bioavailable non-covalent Nrf2 activators

(2019) Bin Ma et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Dynamic Chirality in the Mechanism of Action of Allosteric CD36 Modulators of Macrophage-Driven Inflammation

(2019) Emma Danelius et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of a novel small-molecule Keap1–Nrf2 PPI inhibitor with cytoprotective effects on LPS-induced cardiomyopathy

(2018) Cheng-Shi Jiang et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

In Vitro Intrinsic Permeability: A Transporter-Independent Measure of Caco-2 Cell Permeability in Drug Design and Development

(2017) Linda Fredlund et al.   MOLECULAR PHARMACEUTICS

Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site

(2017) Pierre Matricon et al.   Scientific Reports

Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein–Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery

(2016) Thomas G. Davies et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

(2016) Duncan E. Scott et al.   NATURE REVIEWS DRUG DISCOVERY

Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins

(2016) Emma Danelius et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Probing the structural requirements of non-electrophilic naphthalene-based Nrf2 activators

(2015) Atul D. Jain et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

(2015) Stefan Geschwindner et al.   JOURNAL OF MEDICINAL CHEMISTRY

How Beyond Rule of 5 Drugs and Clinical Candidates Bind to Their Targets

(2015) Bradley C. Doak et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality

(2014) Michelle R. Arkin et al.   CHEMISTRY & BIOLOGY

Discovery of Potent Keap1–Nrf2 Protein–Protein Interaction Inhibitor Based on Molecular Binding Determinants Analysis

(2014) Zheng-Yu Jiang et al.   JOURNAL OF MEDICINAL CHEMISTRY

An NMR Method for the Quantitative Assessment of Intramolecular Hydrogen Bonding; Application to Physicochemical, Environmental, and Biochemical Properties

(2014) Michael H. Abraham et al.   JOURNAL OF ORGANIC CHEMISTRY

How proteins bind macrocycles

(2014) Elizabeth A Villar et al.   Nature Chemical Biology

Kinetic, Thermodynamic, and Structural Characterizations of the Association between Nrf2-DLGex Degron and Keap1

(2013) Toshiaki Fukutomi et al.   MOLECULAR AND CELLULAR BIOLOGY

Synthesis and Application of Palladium Precatalysts that Accommodate Extremely Bulky Di-tert-butylphosphino Biaryl Ligands

(2013) Nicholas C. Bruno et al.   ORGANIC LETTERS

Ligand Pose and Orientational Sampling in Molecular Docking

(2013) Ryan G. Coleman et al.   PLoS One

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Data processing and analysis with theautoPROCtoolbox

(2011) Clemens Vonrhein et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Kinetic Analyses of Keap1-Nrf2 Interaction and Determination of the Minimal Nrf2 Peptide Sequence Required for Keap1 Binding Using Surface Plasmon Resonance

(2011) Yu Chen et al.   Chemical Biology & Drug Design

From Structure Diagrams to Visual Chemical Patterns

(2010) Karen Schomburg et al.   Journal of Chemical Information and Modeling

Rapid Context-Dependent Ligand Desolvation in Molecular Docking

(2010) Michael M. Mysinger et al.   Journal of Chemical Information and Modeling

Disulfide Cyclized Tripeptide Analogues of Angiotensin IV as Potent and Selective Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

(2010) Hanna Andersson et al.   JOURNAL OF MEDICINAL CHEMISTRY

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

(2010) Jonathan B. Baell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Salt bridges: Geometrically specific, designable interactions

(2010) Jason E. Donald et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

EASY ROESY: Reliable Cross-Peak Integration in Adiabatic Symmetrized ROESY

(2008) Christina M. Thiele et al.   CHEMISTRY-A EUROPEAN JOURNAL

The exploration of macrocycles for drug discovery — an underexploited structural class

(2008) Edward M. Driggers et al.   NATURE REVIEWS DRUG DISCOVERY