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

Targeting the Main Protease of SARS‐CoV‐2: From the Establishment of High Throughput Screening to the Design of Tailored Inhibitors

(2021) Julian Breidenbach et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model

(2021) Jingxin Qiao et al.   SCIENCE

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

(2021) Chun-Hui Zhang et al.   ACS Central Science

Drug Development and Medicinal Chemistry Efforts toward SARS‐Coronavirus and Covid‐19 Therapeutics

(2020) Arun K. Ghosh et al.   ChemMedChem

Assessment of Binding Affinity via Alchemical Free Energy Calculations

(2020) Maximilian Kuhn et al.   Journal of Chemical Information and Modeling

Cathepsin L-selective inhibitors: A potentially promising treatment for COVID-19 patients

(2020) Tianxiao Liu et al.   PHARMACOLOGY & THERAPEUTICS

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease

(2020) Wenhao Dai et al.   SCIENCE

Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV

(2020) Xiuyuan Ou et al.   Nature Communications

Mapping the S1 and S1’ subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents

(2020) Lorenzo Cianni et al.   PLoS Neglected Tropical Diseases

Optimization strategy of single-digit nanomolar cross-class inhibitors of mammalian and protozoa cysteine proteases

(2020) Lorenzo Cianni et al.   BIOORGANIC CHEMISTRY

Rigorous Free Energy Simulations in Virtual Screening

(2020) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Evolution of Alchemical Free Energy Methods in Drug Discovery

(2020) Lin Frank Song et al.   Journal of Chemical Information and Modeling

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

Design, synthesis and stepwise optimization of nitrile-based inhibitors of cathepsins B and L

(2020) Lorenzo Cianni et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Activity cliffs produced by single-atom modification of active compounds: Systematic identification and rationalization based on X-ray structures

(2020) Huabin Hu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Exploring the Catalytic Reaction of Cysteine Proteases

(2020) Gabriel Oanca et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting Activity Cliffs with Free-Energy Perturbation

(2019) Laura Pérez-Benito et al.   Journal of Chemical Theory and Computation

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

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

QligFEP: an automated workflow for small molecule free energy calculations in Q

(2019) Willem Jespers et al.   Journal of Cheminformatics

Can Cysteine Protease Cross-class Inhibitors Achieve Selectivity?

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

Hydration of Aromatic Heterocycles as Adversary of π-Stacking

(2019) Johannes Reinhard Loeffler et al.   Journal of Chemical Information and Modeling

QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

(2019) Willem Jespers et al.   Journal of Chemical Theory and Computation

Evolving Concept of Activity Cliffs

(2019) Dagmar Stumpfe et al.   ACS Omega

An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains

(2019) Filip Fratev et al.   Scientific Reports

Catalytic Mechanism of Cruzain from Trypanosoma cruzi As Determined from Solvent Kinetic Isotope Effects of Steady-State and Pre-Steady-State Kinetics

(2018) Xiang Zhai et al.   BIOCHEMISTRY

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

Functional analysis of potential cleavage sites in the MERS-coronavirus spike protein

(2018) Hannah Kleine-Weber et al.   Scientific Reports

Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity

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

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

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

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

(2017) Bernd Kuhn et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

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

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Targeted Covalent Inhibitors for Drug Design

(2016) Thomas A. Baillie   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Design, Synthesis and Trypanocidal Activity of Dipeptidyl Nitriles as Cruzain Inhibitors

(2015) Leandro A. A. Avelar et al.   PLoS Neglected Tropical Diseases

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Exploring Activity Cliffs in Medicinal Chemistry

(2012) Dagmar Stumpfe et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Molecular mechanical study of halogen bonding in drug discovery

(2011) Mahmoud A. A. Ibrahim   JOURNAL OF COMPUTATIONAL CHEMISTRY

The resurgence of covalent drugs

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

Halogen bonding in ligand–receptor systems in the framework of classical force fields

(2011) Stefano Rendine et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions

(2010) Leo A. Hardegger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Principles of early drug discovery

(2010) JP Hughes et al.   BRITISH JOURNAL OF PHARMACOLOGY

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Dipeptidyl nitrile inhibitors of Cathepsin L

(2009) Nabil Asaad et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

How intramembrane proteases bury hydrolytic reactions in the membrane

(2009) Elinor Erez et al.   NATURE