Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces

Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition

(2022) Carlos A. Ramos-Guzmán et al.   Journal of Chemical Theory and Computation

Elucidating the dual mode of action of dipeptidyl enoates in the inhibition of rhodesain cysteine proteases

(2021) Kemel Arafet et al.   CHEMISTRY-A EUROPEAN JOURNAL

Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations

(2021) Vinícius Bonatto et al.   Journal of Chemical Information and Modeling

Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**

(2021) Carlos A. Ramos‐Guzmán et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19

(2021) Dafydd R. Owen et al.   SCIENCE

Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors

(2020) Clauber H. S. da Costa et al.   Journal of Chemical Information and Modeling

ON THE ASSESSMENT OF THE CRUZAIN CYSTEINE PROTEASE REVERSIBLE AND IRREVERSIBLE COVALENT INHIBITION MECHANISM

(2020) José Rogério A. Silva et al.   Journal of Chemical Information and Modeling

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

The SARS-CoV-2 main protease as drug target

(2020) Sven Ullrich et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19

(2020) Robert L. Hoffman et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2

(2020) Dibyendu Mondal et al.   BIOCHEMISTRY

Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations

(2020) Levente M. Mihalovits et al.   Journal of Chemical Information and Modeling

The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K

(2019) Elma Mons et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ranking Reversible Covalent Drugs: From Free Energy Perturbation to Fragment Docking

(2019) Han Zhang et al.   Journal of Chemical Information and Modeling

Characterising covalent warhead reactivity

(2019) James S. Martin et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Pharmacokinetic–pharmacodynamic models that incorporate drug–target binding kinetics

(2019) Fereidoon Daryaee et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Can Cysteine Protease Cross-class Inhibitors Achieve Selectivity?

(2019) Lorenzo Cianni et al.   JOURNAL OF MEDICINAL CHEMISTRY

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics

(2019) Haoyu S. Yu et al.   Journal of Chemical Information and Modeling

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

(2019) Ernest Awoonor‐Williams et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Quantum mechanics/molecular mechanics studies of the mechanism of cysteine proteases inhibition by dipeptidyl nitroalkenes

(2019) Vicent Moliner et al.   CHEMISTRY-A EUROPEAN JOURNAL

The Taxonomy of Covalent Inhibitors

(2018) Alfred Tuley et al.   BIOCHEMISTRY

Structure-based design of targeted covalent inhibitors

(2018) Richard Lonsdale et al.   CHEMICAL SOCIETY REVIEWS

Drug target residence time: a misleading concept

(2018) Rutger H.A. Folmer   DRUG DISCOVERY TODAY

Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles

(2018) Alberto Monteiro Dos Santos et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology

(2018) Matthias Gehringer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Covalent inhibitors design and discovery

(2017) Stephane De Cesco et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity

(2017) Richard Lonsdale et al.   Journal of Chemical Information and Modeling

Unraveling the Addition–Elimination Mechanism of EPSP Synthase through Computer Modeling

(2017) Alberto M. dos Santos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?

(2017) Payal Chatterjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease

(2017) Kemel Arafet et al.   ACS Catalysis

Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins

(2016) Ernest Awoonor-Williams et al.   Journal of Chemical Theory and Computation

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain

(2016) Attila Fekete et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Perspective on the Kinetics of Covalent and Irreversible Inhibition

(2016) John M. Strelow   SLAS Discovery

First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones

(2015) Kemel Arafet et al.   BIOCHEMISTRY

Systematic Study of the Glutathione (GSH) Reactivity of N-Arylacrylamides: 1. Effects of Aryl Substitution

(2015) Victor J. Cee et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of a Potent and Selective EGFR Inhibitor (AZD9291) of Both Sensitizing and T790M Resistance Mutations That Spares the Wild Type Form of the Receptor

(2014) M. Raymond V. Finlay et al.   JOURNAL OF MEDICINAL CHEMISTRY

Chemical and Computational Methods for the Characterization of Covalent Reactive Groups for the Prospective Design of Irreversible Inhibitors

(2014) Mark E. Flanagan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Reaction Pathway and Free Energy Profile for Papain-Catalyzed Hydrolysis of N-Acetyl-Phe-Gly 4-Nitroanilide

(2013) Donghui Wei et al.   BIOCHEMISTRY

Drug discovery considerations in the development of covalent inhibitors

(2013) Robert Mah et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Range-Separated DFT Functionals are Necessary to Model Thio-Michael Additions

(2013) Jennifer M. Smith et al.   Journal of Chemical Theory and Computation

Benchmark Study for the Cysteine–Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches

(2013) Alexander Paasche et al.   Journal of Chemical Theory and Computation

Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase

(2013) Rong-Zhen Liao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Identification of Potent and Selective Cathepsin S Inhibitors Containing Different Central Cyclic Scaffolds

(2013) Hans Hilpert et al.   JOURNAL OF MEDICINAL CHEMISTRY

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

(2013) Jonathan M. Ostrem et al.   NATURE

Transition States, Analogues, and Drug Development

(2012) Vern L. Schramm   ACS Chemical Biology

Understanding the pKa of Redox Cysteines: The Key Role of Hydrogen Bonding

(2012) Goedele Roos et al.   ANTIOXIDANTS & REDOX SIGNALING

Measurement and Estimation of Electrophilic Reactivity for Predictive Toxicology

(2011) Johannes A. H. Schwöbel et al.   CHEMICAL REVIEWS

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Enzyme Molecular Mechanism as a Starting Point to Design New Inhibitors: A Theoretical Study ofO-GlcNAcase

(2011) Jerônimo Lameira et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The resurgence of covalent drugs

(2011) Juswinder Singh et al.   NATURE REVIEWS DRUG DISCOVERY

The discovery of odanacatib (MK-0822), a selective inhibitor of cathepsin K

(2008) Jacques Yves Gauthier et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate

(2008) Anna L. Bowman et al.   CHEMICAL COMMUNICATIONS

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450

(2008) Patrik Rydberg et al.   Journal of Chemical Theory and Computation