Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders

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

(2022) Fabio Begnini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Roles of NRF2 in Fibrotic Diseases: From Mechanisms to Therapeutic Approaches

(2022) Wenlong Hao et al.   Frontiers in Physiology

Pros and cons of NRF2 activation as adjunctive therapy in rheumatoid arthritis

(2022) Gina Manda et al.   FREE RADICAL BIOLOGY AND MEDICINE

Structure-Based Design of Stapled Peptides That Bind GABARAP and Inhibit Autophagy

(2022) Hawley Brown et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate de novo design of membrane-traversing macrocycles

(2022) Gaurav Bhardwaj et al.   CELL

LipoxinA4 analog BML-111 protects podocytes cultured in high-glucose medium against oxidative injury via activating Nrf2 pathway

(2022) Hua Hao et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

KEAP1‐NRF2 protein–protein interaction inhibitors: Design, pharmacological properties and therapeutic potential

(2022) Enrique Crisman et al.   MEDICINAL RESEARCH REVIEWS

Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations

(2021) Jovan Damjanovic et al.   CHEMICAL REVIEWS

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

Stapled peptide inhibitors of autophagy adapter LC3B

(2020) Robert A. Cerulli et al.   CHEMBIOCHEM

Recent progress in Keap1-Nrf2 protein-protein interaction inhibitors

(2020) Yi Mou et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides

(2019) Ashleigh E. Cummings et al.   BIOPHYSICAL JOURNAL

Trapped! A critical evaluation of methods for measuring total cellular uptake versus cytosolic localization

(2019) Kirsten Deprey et al.   BIOCONJUGATE CHEMISTRY

A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies

(2019) Xiaoshu Jing et al.   MEDICINAL RESEARCH REVIEWS

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

Perfluoroarene-based peptide macrocycles that inhibit the Nrf2/Keap1 interaction

(2018) Richard J. Steel et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Understanding and designing head-to-tail cyclic peptides

(2018) Diana P. Slough et al.   BIOPOLYMERS

Modified Peptide Inhibitors of the Keap1-Nrf2 Protein-Protein Interaction Incorporating Unnatural Amino Acids

(2018) Nikolaos D. Georgakopoulos et al.   CHEMBIOCHEM

Discovery of a head-to-tail cyclic peptide as the Keap1-Nrf2 protein-protein interaction inhibitor with high cell potency

(2018) Meng-Chen Lu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach

(2018) Antonio Cuadrado et al.   PHARMACOLOGICAL REVIEWS

Cell Penetration Profiling Using the Chloroalkane Penetration Assay

(2018) Leila Peraro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Constrained peptides' time to shine?

(2018) Chris Morrison   NATURE REVIEWS DRUG DISCOVERY

Perfluoroarene–Based Peptide Macrocycles to Enhance Penetration Across the Blood–Brain Barrier

(2017) Colin M. Fadzen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Diversity-Oriented Stapling Yields Intrinsically Cell-Penetrant Inducers of Autophagy

(2017) Leila Peraro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Mapping the sequence–structure relationships of simple cyclic hexapeptides

(2017) Sean M. McHugh et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Comprehensive computational design of ordered peptide macrocycles

(2017) Parisa Hosseinzadeh et al.   SCIENCE

Insights into How Cyclic Peptides Switch Conformations

(2016) Sean M. McHugh et al.   Journal of Chemical Theory and Computation

Analysis of Loops that Mediate Protein–Protein Interactions and Translation into Submicromolar Inhibitors

(2016) Timothy R. Siegert et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Construction and screening of vast libraries of natural product-like macrocyclic peptides using in vitro display technologies

(2015) Nasir K Bashiruddin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Toward structure prediction of cyclic peptides

(2015) Hongtao Yu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Design of antiviral stapled peptides containing a biphenyl cross-linker

(2014) Avinash Muppidi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

(2014) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

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

Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB

(2014) Chen-Yang Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comprehensive analysis of loops at protein-protein interfaces for macrocycle design

(2014) Jason Gavenonis et al.   Nature Chemical Biology

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model

(2013) João M. Damas et al.   Journal of Chemical Theory and Computation

A Perfluoroaryl-Cysteine SNAr Chemistry Approach to Unprotected Peptide Stapling

(2013) Alexander M. Spokoyny et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Peptide inhibitors of the Keap1–Nrf2 protein–protein interaction with improved binding and cellular activity

(2013) Rowena Hancock et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

(2012) Hyunil Jo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Achieving cell penetration with distance-matching cysteine cross-linkers: a facile route to cell-permeable peptide dual inhibitors of Mdm2/Mdmx

(2011) Avinash Muppidi et al.   CHEMICAL COMMUNICATIONS

Activation of NRF2 by Nitrosative Agents and H2O2Involves KEAP1 Disulfide Formation

(2010) Simon Fourquet et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model

(2010) Pilar Cossio et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phage-encoded combinatorial chemical libraries based on bicyclic peptides

(2009) Christian Heinis et al.   Nature Chemical Biology

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

The Antioxidant Defense System Keap1-Nrf2 Comprises a Multiple Sensing Mechanism for Responding to a Wide Range of Chemical Compounds

(2008) M. Kobayashi et al.   MOLECULAR AND CELLULAR BIOLOGY