G. Tresadern

发表

Constitutive activity of the metabotropic glutamate receptor 2 explored with a whole‐cell label‐free biosensor

A. IJzerman, L. Heitman, M. Doornbos, 2018, Biochemical pharmacology.

Computational Drug Design Applied to the Study of Metabotropic Glutamate Receptors

G. Tresadern, Claudia Llinas Del Torrent, L. Pérez-Benito, 2019, Molecules.

Preparing and Filtering Compound Databases for Virtual and Experimental Screening

J. Wegner, G. Tresadern, M. Cummings, 2011 .

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

P. Coveney, H. V. van Vlijmen, G. Tresadern, 2018, Scientific Reports.

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange

P. Coveney, H. V. van Vlijmen, G. Tresadern, 2019, Advanced theory and simulations.

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Fouad S. Husseini, P. Coveney, H. V. van Vlijmen, 2019, Advanced theory and simulations.

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling

John P. Overington, H. V. van Vlijmen, G. V. van Westen, 2017, J. Chem. Inf. Model..

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study.

Laura Pérez-Benito, Herman W T van Vlijmen, Myriam Ciordia, 2017, Journal of chemical theory and computation.

The computational modeling of allosteric modulation of metabotropic glutamate receptors.

L. Pardo, G. Tresadern, Claudia Llinas Del Torrent, 2020, Advances in pharmacology.

Molecular determinants of positive allosteric modulation of the human metabotropic glutamate receptor 2

G. Tresadern, H. Lavreysen, J. Cid, 2015, British journal of pharmacology.

QSAR design of triazolopyridine mGlu2 receptor positive allosteric modulators.

G. Tresadern, J. Cid, A. A. Trabanco, 2014, Journal of molecular graphics & modelling.

Discovery of 1,4-disubstituted 3-cyano-2-pyridones: a new class of positive allosteric modulators of the metabotropic glutamate 2 receptor.

María Lourdes Linares, J. M. Alonso, G. Macdonald, 2012, Journal of medicinal chemistry.

Discovery of 1,5-disubstituted pyridones: a new class of positive allosteric modulators of the metabotropic glutamate 2 receptor.

María Lourdes Linares, G. Macdonald, G. Tresadern, 2010, ACS chemical neuroscience.

Scaffold hopping from pyridones to imidazo[1,2-a]pyridines. New positive allosteric modulators of metabotropic glutamate 2 receptor.

María Lourdes Linares, G. Macdonald, G. Tresadern, 2010, Bioorganic & medicinal chemistry letters.

Best Practices for Alchemical Free Energy Calculations

Michael R. Shirts, Levi N. Naden, Bryce K. Allen, 2020, 2008.03067.

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

B. L. de Groot, G. Tresadern, V. Gapsys, 2019, Chemical science.

Industrial medicinal chemistry insights: neuroscience hit generation at Janssen.

G. Macdonald, G. Tresadern, Frederik J. R. Rombouts, 2017, Drug discovery today.

Hydride shift in substituted phenyl glyoxals: Interpretation of experimental rate data using electronic structure and variational transition state theory calculations

G. Tresadern, I. H. Hillier, C. I. Watt, 2001 .

Benchmark assessment of molecular geometries and energies from small molecule force fields

David F. Hahn, D. Mobley, C. Bayly, 2020, F1000Research.

Rational design and synthesis of aminopiperazinones as β-secretase (BACE) inhibitors.

J. Spurlino, F. Delgado, Ó. Delgado, 2011, Bioorganic & medicinal chemistry letters.

The facile decomposition of chlorine nitrate in small water clusters

G. Tresadern, I. H. Hillier, J. Mcnamara, 1999 .

Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation

H. V. van Vlijmen, G. Tresadern, Henrik Keränen, 2018, Scientific Reports.

DeltaDelta Neural Networks for Lead Optimization of Small Molecule Potency

G. Tresadern, Rubben Torella, G. de Fabritiis, 2019 .

Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose

G. Tresadern, V. Guallar, Christophe Buyck, 2020, RSC advances.

Imidazo[1,2-a]pyridines: orally active positive allosteric modulators of the metabotropic glutamate 2 receptor.

María Lourdes Linares, Sergio A Alonso de Diego, J. M. Alonso, 2012, Journal of medicinal chemistry.

Teaser Modern medicinal chemistry impacts drug discovery in many ways beyond just optimization of clinical candidates

G. Macdonald, G. Tresadern, Frederik J. R. Rombouts, 2017 .

Molecular properties affecting fast dissociation from the D2 receptor.

X. Langlois, G. Macdonald, G. Tresadern, 2011, Bioorganic & medicinal chemistry.

Molecular Switches of Allosteric Modulation of the Metabotropic Glutamate 2 Receptor.

Arnau Cordomí, Leonardo Pardo, Laura Pérez-Benito, 2017, Structure.

Covalent Allosteric Probe for the Metabotropic Glutamate Receptor 2: Design, Synthesis, and Pharmacological Characterization

A. IJzerman, L. Heitman, M. Doornbos, 2018, Journal of medicinal chemistry.

Progress in the developement of positive allosteric modulators of the metabotropic glutamate receptor 2.

G. Macdonald, G. Tresadern, H. Lavreysen, 2011, Current medicinal chemistry.

Extending kinome coverage by analysis of kinase inhibitor broad profiling data.

Edgar Jacoby, Jean-Marc Neefs, Dmitrii Rassokhin, 2015, Drug discovery today.

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors

Laura Pérez-Benito, Myriam Ciordia, Francisca Delgado, 2016, J. Chem. Inf. Model..

Scenarios and Case Studies: Examples for Ligand‐Based Virtual Screening

Gary Tresadern, Daniele Bemporad, Trevor Howe, 2011 .

triazolo [ 4 , 3 ‐ a ] pyrazines as Selective , Brain Penetrant Phosphodiesterase 2 ( PDE 2 ) Inhibitors

X. Langlois, M. Somers, G. Vanhoof, 2015 .

A comparison of ligand based virtual screening methods and application to corticotropin releasing factor 1 receptor.

Gary Tresadern, Daniele Bemporad, Trevor Howe, 2009, Journal of molecular graphics & modelling.

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Agastya P. Bhati, P. Coveney, H. V. van Vlijmen, 2022, Scientific Reports.

A phenotypic high-content, high-throughput screen identifies inhibitors of NLRP3 inflammasome activation

D. Brough, G. Tresadern, P. Brennan, 2021, Scientific Reports.

Design and synthesis of a novel series of bicyclic heterocycles as potent γ-secretase modulators.

G. Macdonald, G. Tresadern, M. Mercken, 2012, Journal of medicinal chemistry.

A LiveCoMS Best Practices Guide Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.2]

David F. Hahn, D. Mobley, J. Chodera, 2021 .

Chemical Space Exploration with Active Learning and Alchemical Free Energies

David F. Hahn, B. L. de Groot, G. Tresadern, 2022, Journal of chemical theory and computation.

A Free Energy Perturbation Approach to Estimate the Intrinsic Solubilities of Drug-like Small Molecules

G. Tresadern, R. Farid, J. Greenwood, 2019 .

DeltaDelta neural networks for lead optimization of small molecule potency† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c9sc04606b

G. Tresadern, Rubben Torella, G. de Fabritiis, 2019, Chemical science.

Diazaspirononane Nonsaccharide Inhibitors of O-GlcNAcase (OGA) for the Treatment of Neurodegenerative Disorders.

J. Bartolomé-Nebreda, F. Delgado, Carlos M Martínez-Viturro, 2020, Journal of medicinal chemistry.

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations

Rebecca M. Twidale, H. V. van Vlijmen, G. Tresadern, 2020, Chemical science.

Evaluation of a Series of β-Secretase 1 Inhibitors Containing Novel Heteroaryl-Fused-Piperazine Amidine Warheads.

Sergio A Alonso de Diego, Michiel Van Gool, G. Macdonald, 2019, ACS Medicinal Chemistry Letters.

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field

David L. Dotson, S. K. Lakkaraju, Joshua T. Horton, 2022, J. Chem. Inf. Model..

Benchmark assessment of molecular geometries and energies from small molecule force fields

Victoria T. Lim, David F. Hahn, D. Mobley, 2020, F1000Research.

Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme

G. Tresadern, A. Pineda-Lucena, G. de Fabritiis, 2016, Scientific Reports.

Discovery of 8-Trifluoromethyl-3-cyclopropylmethyl-7-[(4-(2,4-difluorophenyl)-1-piperazinyl)methyl]-1,2,4-triazolo[4,3-a]pyridine (JNJ-46356479), a Selective and Orally Bioavailable mGlu2 Receptor Positive Allosteric Modulator (PAM).

María Lourdes Linares, G. Macdonald, M. Somers, 2016, Journal of medicinal chemistry.

1,4-Oxazine β-Secretase 1 (BACE1) Inhibitors: From Hit Generation to Orally Bioavailable Brain Penetrant Leads.

Ó. Delgado, Michiel Van Gool, J. M. Alonso, 2015, Journal of medicinal chemistry.

Benzazaborinines as Novel Bioisosteric Replacements of Naphthalene: Propranolol as an Example.

G. Tresadern, Frederik J. R. Rombouts, N. Austin, 2015, Journal of medicinal chemistry.

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer

Rodrigo F. Ortiz-Meoz, J. C. Gómez-Tamayo, A. Thompson, 2022, Heliyon.

Structures of human Malic Enzyme 3

Rodrigo F. Ortiz-Meoz, J. C. Gómez-Tamayo, A. Thompson, 2022, bioRxiv.

Anilinotriazoles as potent gamma secretase modulators.

G. Macdonald, G. Tresadern, M. Mercken, 2014, Bioorganic & medicinal chemistry letters.

[1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration.

G. Macdonald, M. Somers, G. Vanhoof, 2020, Journal of medicinal chemistry.

An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase

G. Tresadern, N. Burton, I. H. Hillier, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Recognizing Pitfalls in Virtual Screening: A Critical Review

Andreas Bender, Dimitris K. Agrafiotis, Thierry Langer, 2012, J. Chem. Inf. Model..

Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors

Adrian J. Mulholland, Herman van Vlijmen, Gary Tresadern, 2019, J. Chem. Inf. Model..

Molecular blueprint of allosteric binding sites in a homologue of the agonist-binding domain of the α7 nicotinic acetylcholine receptor

D. Bertrand, G. Tresadern, C. Ulens, 2015, Proceedings of the National Academy of Sciences.

Fragment Binding to β-Secretase 1 without Catalytic Aspartate Interactions Identified via Orthogonal Screening Approaches

G. Tresadern, A. Pineda-Lucena, D. Moechars, 2017, ACS omega.

Selective inhibition of intestinal guanosine 3′,5′-cyclic monophosphate signaling by small-molecule protein kinase inhibitors

G. Tresadern, J. Schuurkes, K. Smans, 2018, The Journal of Biological Chemistry.

Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery

E. Jacoby, G. Tresadern, J. Harvey, 2022, J. Chem. Inf. Model..

Design, synthesis, and biological evaluation of novel fluorinated ethanolamines.

Ó. Delgado, G. Tresadern, M. Gütschow, 2011, Chemistry.

Direct dynamics calculations of reaction rate and kinetic isotope effects in enzyme catalysed reactions.

G. Tresadern, N. Burton, I. H. Hillier, 2003, Faraday discussions.

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].

David F. Hahn, D. Mobley, J. Chodera, 2021, Living journal of computational molecular science.

Alchemical absolute protein–ligand binding free energies for drug design

D. Mobley, B. L. de Groot, G. Tresadern, 2021, Chemical science.

Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use

Dimitris K. Agrafiotis, Gary Tresadern, D. Agrafiotis, 2009, J. Chem. Inf. Model..

Inhibition of the Alanine-Serine-Cysteine-1 Transporter by BMS-466442.

L. Pardo, Susana Conde-Ceide, G. Tresadern, 2019, ACS chemical neuroscience.

Structure-Based Design of a Potent, Selective, and Brain Penetrating PDE2 Inhibitor with Demonstrated Target Engagement.

X. Langlois, G. Vanhoof, G. Tresadern, 2014, ACS medicinal chemistry letters.

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

B. L. de Groot, G. Tresadern, Vytautas Gapsys, 2020, Journal of Computer-Aided Molecular Design.

Product ion mobility as a promising tool for assignment of positional isomers of drug metabolites.

G. Tresadern, R. Mortishire-Smith, C. Wassvik, 2011, Rapid communications in mass spectrometry : RCM.

Discovery of 3-cyclopropylmethyl-7-(4-phenylpiperidin-1-yl)-8-trifluoromethyl[1,2,4]triazolo[4,3-a]pyridine (JNJ-42153605): a positive allosteric modulator of the metabotropic glutamate 2 receptor.

María Lourdes Linares, A. Megens, G. Macdonald, 2012, Journal of medicinal chemistry.

Scaffold Hopping to Imidazo[1,2-a]pyrazin-8-one Positive Allosteric Modulators of Metabotropic Glutamate 2 Receptor

María Lourdes Linares, G. Tresadern, H. Lavreysen, 2021, ACS omega.

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

David F. Hahn, D. Mobley, B. L. de Groot, 2022, J. Chem. Inf. Model..

To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough

David F. Hahn, D. Mobley, G. Tresadern, 2023, J. Chem. Inf. Model..

Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation

H. V. van Vlijmen, G. Tresadern, Henrik Keränen, 2018, Scientific Reports.

The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions

H. V. van Vlijmen, G. Tresadern, H. Geys, 2022, J. Chem. Inf. Model..

Predicting Activity Cliffs with Free-Energy Perturbation.

Mireia Jiménez-Rosés, Laura Pérez-Benito, Gary Tresadern, 2019, Journal of chemical theory and computation.

Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation

Chris de Graaf, Herman van Vlijmen, Jonathan S. Mason, 2020, J. Chem. Inf. Model..

Pyrido[4,3-e][1,2,4]triazolo[4,3-a]pyrazines as Selective, Brain Penetrant Phosphodiesterase 2 (PDE2) Inhibitors.

X. Langlois, G. Vanhoof, G. Tresadern, 2015, ACS medicinal chemistry letters.

Spiro-oxindole Piperidines and 3-(Azetidin-3-yl)-1H-benzimidazol-2-ones as mGlu2 Receptor PAMs.

María Lourdes Linares, G. Tresadern, H. Lavreysen, 2019, ACS medicinal chemistry letters.

Discovery and Kinetic Profiling of 7-Aryl-1,2,4-triazolo[4,3-a]pyridines: Positive Allosteric Modulators of the Metabotropic Glutamate Receptor 2.

A. IJzerman, T. Mulder-Krieger, L. Heitman, 2017, Journal of medicinal chemistry.

Molecular mechanism of positive allosteric modulation of the metabotropic glutamate receptor 2 by JNJ‐46281222

A. IJzerman, T. Mulder-Krieger, L. Heitman, 2016, British journal of pharmacology.

Discovery of 1-butyl-3-chloro-4-(4-phenyl-1-piperidinyl)-(1H)-pyridone (JNJ-40411813): a novel positive allosteric modulator of the metabotropic glutamate 2 receptor.

María Lourdes Linares, J. M. Alonso, G. Macdonald, 2014, Journal of medicinal chemistry.

Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5

Leonardo Pardo, Laura Pérez-Benito, Gary Tresadern, 2019, J. Chem. Inf. Model..

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

Levi N. Naden, Bryce K. Allen, David F. Hahn, 2019, Living Journal of Computational Molecular Science.

Recent advances in quantum mechanical/molecular mechanical calculations of enzyme catalysis: hydrogen tunnelling in liver alcohol dehydrogenase and inhibition of elastase by α-ketoheterocycles

G. Tresadern, N. Burton, M. P. Gleeson, 2003 .

Impact of allosteric modulation: Exploring the binding kinetics of glutamate and other orthosteric ligands of the metabotropic glutamate receptor 2

A. IJzerman, L. Heitman, G. Tresadern, 2018, Biochemical pharmacology.

Design and synthesis of bicyclic heterocycles as potent γ-secretase modulators.

G. Macdonald, G. Tresadern, M. Mercken, 2013, Bioorganic & medicinal chemistry letters.

A Brain-Penetrant and Bioavailable Pyrazolopiperazine BACE1 Inhibitor Elicits Sustained Reduction of Amyloid β In Vivo.

Michiel Van Gool, G. Macdonald, G. Tresadern, 2021, ACS medicinal chemistry letters.

A Versatile Approach to CF3 -Containing 2-Pyrrolidones by Tandem Michael Addition-Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors.

Ó. Delgado, Michiel Van Gool, G. Tresadern, 2015, Chemistry.

mGlu2 Receptor Agonism, but Not Positive Allosteric Modulation, Elicits Rapid Tolerance towards Their Primary Efficacy on Sleep Measures in Rats

G. Tresadern, H. Lavreysen, W. Drinkenburg, 2015, PloS one.

The prokaryote ligand-gated ion channel ELIC captured in a pore blocker-bound conformation by the Alzheimer's disease drug memantine.

G. Tresadern, C. Ulens, A. J. Thompson, 2014, Structure.

Dihydrothiazolopyridone derivatives as a novel family of positive allosteric modulators of the metabotropic glutamate 5 (mGlu5) receptor.

S. Jadhav, J. Bartolomé-Nebreda, F. Delgado, 2013, Journal of medicinal chemistry.

Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach

Christopher L. McClendon, Frank C. Pickard, David F. Hahn, 2023, Journal of chemical theory and computation.

The size matters? A computational tool to design bivalent ligands

Andrew Henry, Minos-Timotheos Matsoukas, Arnau Cordomí, 2018, Bioinform..

Computationally Guided Identification of Allosteric Agonists of the Metabotropic Glutamate 7 Receptor.

A. Fontana, G. Tresadern, H. Lavreysen, 2018, ACS chemical neuroscience.

Selective inhibitors of the PSEN1–gamma-secretase complex

B. de Strooper, G. Tresadern, V. Guallar, 2023, The Journal of biological chemistry.

Modeling approaches for ligand-based 3D similarity.

Gary Tresadern, Daniele Bemporad, G. Tresadern, 2010, Future medicinal chemistry.

A Versatile Approach to CF3 -Containing 2-Pyrrolidones by Tandem Michael Addition-Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors.

Ó. Delgado, Michiel Van Gool, G. Tresadern, 2015, Chemistry.

A Versatile Approach to CF3‐Containing 2‐Pyrrolidones by Tandem Michael Addition—Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors.

Ó. Delgado, G. Tresadern, L. Pérez-Benito, 2016 .

Best Practices for Alchemical Free Energy Calculations [Article v1.0].

Michael R. Shirts, Levi N. Naden, Bryce K. Allen, 2020, Living journal of computational molecular science.

Alchemical Free Energy Calculations on Membrane-Associated Proteins

H. V. van Vlijmen, P. Matricon, G. Tresadern, 2023, Journal of chemical theory and computation.

MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands

G. Tresadern, Sandeep Somani, James C Robertson, 2023, J. Chem. Inf. Model..

A LiveCoMS Best Practices Guide Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]

C. Bayly, G. Tresadern, A. Mey, 2021 .

Imidazo[1,2-a]pyridines: orally active positive allosteric modulators of the metabotropic glutamate 2 receptor.

María Lourdes Linares, J. M. Alonso, G. Macdonald, 2012, Journal of medicinal chemistry.

Extreme tunnelling in methylamine dehydrogenase revealed by hybrid QM/MM calculations: potential energy surface profile for methylamine and ethanolamine substrates and kinetic isotope effect values

Gary Tresadern, Neil A. Burton, G. Tresadern, 2003 .

Calculations of hydrogen tunnelling and enzyme catalysis: A comparison of liver alcohol dehydrogenase, methylamine dehydrogenase and soybean lipoxygenase

Hong Wang, G. Tresadern, N. Burton, 2002 .

The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks

J. C. Gómez-Tamayo, G. Tresadern, Samia Aci-Sèche, 2023, International journal of molecular sciences.

QM/MM studies show substantial tunneling for the hydrogen-transfer reaction in methylamine dehydrogenase.

Kamaldeep K. Chohan, Nigel S. Scrutton, Gary Tresadern, 2001, Journal of the American Chemical Society.

Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules

G. Tresadern, L. Pérez-Benito, L. Medrano Sandonas, 2024, Scientific data.