Unbinding Kinetics of Muscarinic M3 Receptor Antagonists Explained by Metadynamics Simulations

Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents

(2023) Kemel Arafet et al.   Journal of Chemical Information and Modeling

Discovery of Clinical Candidate CHF-6366: A Novel Super-soft Dual Pharmacology Muscarinic Antagonist and β2 Agonist (MABA) for the Inhaled Treatment of Respiratory Diseases

(2022) Laura Carzaniga et al.   JOURNAL OF MEDICINAL CHEMISTRY

Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective

(2022) Katya Ahmad et al.   Frontiers in Molecular Biosciences

G Protein-Coupled Receptor–Ligand Dissociation Rates and Mechanisms from τRAMD Simulations

(2021) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space

(2021) Chao Lu et al.   Journal of Chemical Theory and Computation

Discovery of M3 Antagonist-PDE4 Inhibitor Dual Pharmacology Molecules for the Treatment of Chronic Obstructive Pulmonary Disease

(2021) Elisabetta Armani et al.   JOURNAL OF MEDICINAL CHEMISTRY

Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors

(2021) Gian Marco Elisi et al.   Journal of Chemical Information and Modeling

A Supervised Molecular Dynamics Approach to Unbiased Ligand-Protein Unbinding

(2020) Giuseppe Deganutti et al.   Journal of Chemical Information and Modeling

Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach

(2020) Surl-Hee Ahn et al.   Journal of Chemical Information and Modeling

Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study

(2020) Riccardo Capelli et al.   Journal of Physical Chemistry Letters

A combined activation mechanism for the glucagon receptor

(2020) Giulio Mattedi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

(2020) Sergio Decherchi et al.   CHEMICAL REVIEWS

Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations

(2019) Riccardo Capelli et al.   Journal of Chemical Theory and Computation

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders

(2019) Andrew Potterton et al.   Journal of Chemical Theory and Computation

Second M 3 muscarinic receptor binding site contributes to bronchoprotection by tiotropium

(2019) Loes E.M. Kistemaker et al.   BRITISH JOURNAL OF PHARMACOLOGY

Investigating Drug–Target Residence Time in Kinases through Enhanced Sampling Simulations

(2019) Dorothea Gobbo et al.   Journal of Chemical Theory and Computation

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

(2018) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists

(2018) Hongtao Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metadynamics Simulations Distinguish Short- and Long-Residence-Time Inhibitors of Cyclin-Dependent Kinase 8

(2017) Donatella Callegari et al.   Journal of Chemical Information and Modeling

Characterizing Drug–Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches

(2017) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Metadynamics for Perspective Drug Design: Computationally Driven Synthesis of New Protein–Protein Interaction Inhibitors Targeting the EphA2 Receptor

(2017) Matteo Incerti et al.   JOURNAL OF MEDICINAL CHEMISTRY

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations

(2017) Rodrigo Casasnovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recent advances in dynamic docking for drug discovery

(2017) Marco De Vivo et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Equilibrium and kinetic selectivity profiling on the human adenosine receptors

(2016) Dong Guo et al.   BIOCHEMICAL PHARMACOLOGY

Exploiting Free-Energy Minima to Design Novel EphA2 Protein-Protein Antagonists: From Simulation to Experiment and Return

(2016) Simonetta Russo et al.   CHEMISTRY-A EUROPEAN JOURNAL

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Free-energy studies reveal a possible mechanism for oxidation-dependent inhibition of MGL

(2016) Laura Scalvini et al.   Scientific Reports

Design strategies to address kinetics of drug binding and residence time

(2015) Kevin P. Cusack et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Decoding the Role of Water Dynamics in Ligand–Protein Unbinding: CRF1R as a Test Case

(2015) Andrea Bortolato et al.   Journal of Chemical Information and Modeling

The drug–target residence time model: a 10-year retrospective

(2015) Robert A. Copeland   NATURE REVIEWS DRUG DISCOVERY

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

(2015) Kalli Kappel et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

(2015) Luca Mollica et al.   Scientific Reports

What can we learn from molecular dynamics simulations for GPCR drug design?

(2015) Christofer S. Tautermann et al.   Computational and Structural Biotechnology Journal

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

(2014) Andrea Cavalli et al.   ACCOUNTS OF CHEMICAL RESEARCH

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

(2014) Matteo Salvalaglio et al.   Journal of Chemical Theory and Computation

Drug-Target Residence Time-A Case for G Protein-Coupled Receptors

(2014) Dong Guo et al.   MEDICINAL RESEARCH REVIEWS

Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis

(2014) Thor Seneca Thorsen et al.   STRUCTURE

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

Pharmacokinetics and the drug–target residence time concept

(2013) Göran Dahl et al.   DRUG DISCOVERY TODAY

Molecular Basis for the Long Duration of Action and Kinetic Selectivity of Tiotropium for the Muscarinic M3 Receptor

(2013) Christofer S. Tautermann et al.   JOURNAL OF MEDICINAL CHEMISTRY

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Structure and dynamics of the M3 muscarinic acetylcholine receptor

(2012) Andrew C. Kruse et al.   NATURE

Inhalation by Design: Novel Tertiary Amine Muscarinic M3Receptor Antagonists with Slow Off-Rate Binding Kinetics for Inhaled Once-Daily Treatment of Chronic Obstructive Pulmonary Disease

(2011) Paul A. Glossop et al.   JOURNAL OF MEDICINAL CHEMISTRY

Investigating the Mechanism of Substrate Uptake and Release in the Glutamate Transporter Homologue GltPh through Metadynamics Simulations

(2011) Giovanni Grazioso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

Drug–target residence time: critical information for lead optimization

(2010) Hao Lu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Binding kinetics and mechanism of action: toward the discovery and development of better and best in class drugs

(2010) Rumin Zhang et al.   Expert Opinion on Drug Discovery

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

(2010) Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

(2010) Jianxin Duan et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Exploring the Mechanism of Agonist Efficacy: A Relationship between Efficacy and Agonist Dissociation Rate at the Muscarinic M3 Receptor

(2009) D. A. Sykes et al.   MOLECULAR PHARMACOLOGY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS