Design of Drug Efficacy Guided by Free Energy Simulations of the β₂-Adrenoceptor

Panel, Nicolas; Vo, Duc Duy; Kahlous, Nour Aldin; Hübner, Harald et al.

Part of Angewandte Chemie International Edition, 2023

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Development and Characterization of Novel Selective, Non-Basic Dopamine D-2 Receptor Antagonists for the Treatment of Schizophrenia

Stepnicki, Piotr; Wosko, Sylwia; Bartyzel, Agata; Zieba, Agata et al.

Part of Molecules, 2023

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Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system

Suades, Albert; Qureshi, Aziz; McComas, Sarah E.; Coincon, Mathieu et al.

Part of Nature Communications, 2023

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Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists

Matricon, Pierre; Nguyen, Anh T. N.; Vo, Duc Duy; Baltos, Jo-Anne et al.

Part of European Journal of Medicinal Chemistry, 2023

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

Begnini, Fabio; Geschwindner, Stefan; Johansson, Patrik; Wissler, Lisa et al.

Part of Journal of Medicinal Chemistry, p. 3473-3517, 2022

• DOI for Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction
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Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5

Kampen, Stefanie; Rodriguez, David; Jorgensen, Morten; Kruszyk-Kujawa, Monika et al.

Part of ACS Chemical Biology, p. 2744-2752, 2022

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The mGlu₅ Receptor Protomer-Mediated Dopamine D₂ Receptor Trans-Inhibition Is Dependent on the Adenosine A_2A Receptor Protomer: Implications for Parkinson's Disease

Romero-Fernandez, Wilber; Taura, Jaume J.; Crans, Rene A. J.; Lopez-Cano, Marc et al.

Part of Molecular Neurobiology, p. 5955-5969, 2022

• DOI for The mGlu₅ Receptor Protomer-Mediated Dopamine D₂ Receptor Trans-Inhibition Is Dependent on the Adenosine A_2A Receptor Protomer: Implications for Parkinson's Disease
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Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Luttens, Andreas; Gullberg, Hjalmar; Abdurakhmanov, Eldar; Vo, Duy Duc et al.

Part of Journal of the American Chemical Society, p. 2905-2920, 2022

• DOI for Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses
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A practical guide to large-scale docking

Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun et al.

Part of Nature Protocols, p. 4799-4832, 2021

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Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Kapla, Jon; Rodriguez Espigares, Ismael; Ballante, Flavio; Selent, Jana et al.

Part of PloS Computational Biology, 2021

• DOI for Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
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Fragment-based design of selective GPCR ligands guided by free energy simulations

Matricon, Pierre; Vo, Duc Duy; Gao, Zhan-Guo; Kihlberg, Jan et al.

Part of Chemical Communications, p. 12305-12308, 2021

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Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

Fleetwood, Oliver; Carlsson, Jens; Delemotte, Lucie

Part of eLIFE, 2021

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Ligand design by targeting a binding site water

Matricon, Pierre; Suresh, R. Rama; Gao, Zhan-Guo; Panel, Nicolas et al.

Part of Chemical Science, p. 960-968, 2021

• DOI for Ligand design by targeting a binding site water

Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia

Draper-Joyce, Christopher J.; Bhola, Rebecca; Wang, Jinan; Bhattarai, Apurba et al.

Part of Nature, p. 571-576, 2021

• DOI for Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia

Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

Kampen, Stefanie; Vo, Duc Duy; Zhang, Xiaoqun; Panel, Nicolas et al.

Part of Angewandte Chemie International Edition, p. 18022-18030, 2021

• DOI for Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology
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Docking Finds GPCR Ligands in Dark Chemical Matter

Ballante, Flavio; Rudling, Axel; Zeifman, Alexey; Luttens, Andreas et al.

Part of Journal of Medicinal Chemistry, p. 613-620, 2020

• DOI for Docking Finds GPCR Ligands in Dark Chemical Matter

Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches

Fleetwood, Oliver; Matricon, Pierre; Carlsson, Jens; Delemotte, Lucie

Part of Biochemistry, p. 880-891, 2020

• DOI for Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches
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GPCRmd uncovers the dynamics of the 3D-GPCRome

Rodriguez-Espigares, Ismael; Torrens-Fontanals, Mariona; Tiemann, Johanna K. S.; Aranda-Garcia, David et al.

Part of Nature Methods, p. 777-787, 2020

• DOI for GPCRmd uncovers the dynamics of the 3D-GPCRome

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

Jaiteh, Mariama; Rodríguez-Espigares, Ismael; Selent, Jana; Carlsson, Jens

Part of PloS Computational Biology, 2020

• DOI for Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity
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The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling

Sommer, Martha E.; Selent, Jana; Carlsson, Jens; De Graaf, Chris et al.

Part of ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE, p. 361-370, 2020

• DOI for The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling
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A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection

Wright, Shane C.; Kozielewicz, Pawel; Kowalski-Jahn, Maria; Petersen, Julian et al.

Part of Nature Communications, 2019

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Disruption of A2AR-D2R Heteroreceptor Complexes After A2AR Transmembrane 5 Peptide Administration Enhances Cocaine Self-Administration in Rats

Borroto-Escuela, Dasiel O.; Wydra, Karolina; Li, Xiang; Rodriguez, David et al.

Part of Molecular Neurobiology, p. 7038-7048, 2018

• DOI for Disruption of A2AR-D2R Heteroreceptor Complexes After A2AR Transmembrane 5 Peptide Administration Enhances Cocaine Self-Administration in Rats
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Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease

Jaiteh, Mariama; Zeifman, Alexey; Saarinen, Marcus; Svenningsson, Per et al.

Part of Journal of Medicinal Chemistry, p. 5269-5278, 2018

• DOI for Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease

FZD(5) is a G alpha(q)-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs

Wright, Shane C.; Canizal, Maria Consuelo Alonso; Benkel, Tobias; Simon, Katharina et al.

Part of Science Signaling, 2018

• DOI for FZD(5) is a G alpha(q)-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs

Mapping the Interface of a GPCR Dimer: A Structural Model of the A(2A) Adenosine and D-2 Dopamine Receptor Heteromer

Borroto-Escuela, Dasiel O.; Rodriguez, David; Romero Fernandez, Wilber; Kapla, Jon et al.

Part of Frontiers in Pharmacology, 2018

• DOI for Mapping the Interface of a GPCR Dimer: A Structural Model of the A(2A) Adenosine and D-2 Dopamine Receptor Heteromer
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Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

Rudling, Axel; Orro, Adolfo; Carlsson, Jens

Part of Journal of Chemical Information and Modeling, p. 350-361, 2018

• DOI for Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

Scavenging of superoxide by a membrane-bound superoxide oxidase

Lundgren, Camilla A. K.; Sjostrand, Dan; Biner, Olivier; Bennett, Matthew et al.

Part of Nature Chemical Biology, p. 788-793, 2018

• DOI for Scavenging of superoxide by a membrane-bound superoxide oxidase

Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling

Kennedy, Amanda; Ballante, Flavio; Johansson, Johan; Milligan, Graeme et al.

Part of ACS Pharmacology & Translational Science, p. 119-133, 2018

• DOI for Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling
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Structure-based screening for GPCR ligands from fragment and lead-like chemical space

Carlsson, Jens

Part of Abstracts of Papers of the American Chemical Society, 2018

Structure-guided discovery of adenosine receptor ligands

Carlsson, Jens

Part of Purinergic Signalling Purinergic Signalling, 2018

• DOI for Structure-guided discovery of adenosine receptor ligands

Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

Petersen, Julian; Wright, Shane C.; Rodriguez, David; Matricon, Pierre et al.

Part of Nature Communications, 2017

• DOI for Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling
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Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site

Matricon, Pierre; Ranganathan, Anirudh; Warnick, Eugene; Gao, Zhan-Guo et al.

Part of Scientific Reports, 2017

• DOI for Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site
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Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space

Rudling, Axel; Gustafsson, Robert; Almlof, Ingrid; Homan, Evert et al.

Part of Journal of Medicinal Chemistry, p. 8160-8169, 2017

• DOI for Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space

Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries

Ranganathan, Anirudh; Heine, Philipp; Rudling, Axel; Pluckthun, Andreas et al.

Part of ACS Chemical Biology, p. 735-745, 2017

• DOI for Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries

Structure-Guided Screening for Functionally Selective D-2 Dopamine Receptor Ligands from a Virtual Chemical Library

Mannel, Barbara; Jaiteh, Mariama; Zeifman, Alexey; Randakova, Alena et al.

Part of ACS Chemical Biology, p. 2652-2661, 2017

• DOI for Structure-Guided Screening for Functionally Selective D-2 Dopamine Receptor Ligands from a Virtual Chemical Library

The tyrosine Y250(2.39) in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled

Strakova, Katerina; Matricon, Pierre; Yokota, Chika; Arthofer, Elisa et al.

Part of Cellular Signalling, p. 85-96, 2017

• DOI for The tyrosine Y250(2.39) in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled

Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists

Rodriguez, David; Chakraborty, Saibal; Warnick, Eugene; Crane, Steven et al.

Part of ACS Chemical Biology, p. 2763-2772, 2016

• DOI for Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists

Discovery of trace amine-associated receptor 1 ligands by molecular docking screening against a homology model

Lam, V. M.; Rodriguez, D.; Zhang, T.; Koh, E. J. et al.

Part of MedChemComm, p. 2216-2223, 2015

• DOI for Discovery of trace amine-associated receptor 1 ligands by molecular docking screening against a homology model

Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models

Ranganathan, Anirudh; Stoddart, Leigh A.; Hill, Stephen J.; Carlsson, Jens

Part of Journal of Medicinal Chemistry, p. 9578-9590, 2015

• DOI for Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Part of Journal of Physical Chemistry B, p. 10255-10260, 2009

• DOI for Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method

Wallin, Göran; Nervall, Martin; Carlsson, Jens; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 380-395, 2009

• DOI for Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method

Predicting Binding Modes from Free Energy Calculations

Nervall, Martin; Hanspers, Peter; Carlsson, Jens; Boukharta, Lars et al.

Part of Journal of Medicinal Chemistry, p. 2657-2667, 2008

• DOI for Predicting Binding Modes from Free Energy Calculations

Active site of epoxide hydrolases revisited: A noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate

Thomaeus, Ann; Carlsson, Jens; Åqvist, Johan; Widersten, Mikael

Part of Biochemistry, p. 2466-2479, 2007

• DOI for Active site of epoxide hydrolases revisited: A noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate

Improving the accuracy of the linear interaction energy method for solvation free energies

Almlöf, Martin; Carlsson, Jens; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 2162-2175, 2007

• DOI for Improving the accuracy of the linear interaction energy method for solvation free energies

Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis

Henriksson, Lena M.; Unge, Torsten; Carlsson, Jens; Åqvist, Johan et al.

Part of Journal of Biological Chemistry, p. 19905-19916, 2007

• DOI for Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis

Calculations of solute and solvent entropies from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Part of Physical Chemistry, Chemical Physics - PCCP, p. 5385-5395, 2006

• DOI for Calculations of solute and solvent entropies from molecular dynamics simulations