71 results on '"Eelke B. Lenselink"'
Search Results
2. Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations.
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Wei Chen, Di Cui, Steven V. Jerome, Mayako Michino, Eelke B. Lenselink, David J. Huggins, Alexandre Beautrait, Jeremie Vendome, Robert Abel, Richard A. Friesner, and Lingle Wang
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- 2023
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3. Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells.
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Olivier J. M. Béquignon, Jose C. Gómez-Tamayo, Eelke B. Lenselink, Steven Wink, Steven Hiemstra, Chi Chung Lam, Domenico Gadaleta, Alessandra Roncaglioni, Ulf Norinder, Bob van de Water, Manuel Pastor, and Gerard J. P. van Westen
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- 2023
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4. Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge.
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Eelke B. Lenselink and Pieter F. W. Stouten
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- 2021
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5. Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors.
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Lindsey Burggraaff, Eelke B. Lenselink, Willem Jespers, Jesper E. van Engelen, Brandon J. Bongers, Marina Gorostiola González, Rongfang Liu, Holger H. Hoos, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Gerard J. P. van Westen
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- 2020
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6. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation.
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Francesca Deflorian, Laura Pérez-Benito, Eelke B. Lenselink, Miles Congreve, Herman W. T. van Vlijmen, Jonathan S. Mason, Chris de Graaf, and Gary Tresadern
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- 2020
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7. Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis
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Tom van der Wel, Riet Hilhorst, Hans den Dulk, Tim van den Hooven, Nienke M. Prins, Joost A. P. M. Wijnakker, Bogdan I. Florea, Eelke B. Lenselink, Gerard J. P. van Westen, Rob Ruijtenbeek, Herman S. Overkleeft, Allard Kaptein, Tjeerd Barf, and Mario van der Stelt
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Science - Abstract
Chemical tools to monitor drug-target engagement of endogenous enzymes are essential for preclinical target validation. Here, the authors present a chemical genetics strategy to study target engagement of endogenous kinases, achieving specific labeling and inactivation of FES kinase to provide insights into FES’ role in neutrophil phagocytosis.
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- 2020
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8. Application of portfolio optimization to drug discovery.
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Iryna Yevseyeva, Eelke B. Lenselink, Alice de Vries, Adriaan P. IJzerman, André H. Deutz, and Michael T. M. Emmerich
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- 2019
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9. Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes.
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Antonius P. A. Janssen, Sebastian H. Grimm, Ruud H. M. Wijdeven, Eelke B. Lenselink, Jacques Neefjes, Constant A. A. van Boeckel, Gerard J. P. van Westen, and Mario van der Stelt
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- 2019
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10. Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
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Eelke B. Lenselink, Niels ten Dijke, Brandon Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, and Gerard J. P. van Westen
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Deep neural networks ,ChEMBL ,QSAR ,Proteochemometrics ,Chemogenomics ,Cheminformatics ,Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Abstract
Abstract The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multitude of different methods have been reported and evaluated, such as target fishing, nearest neighbor similarity-based methods, and Quantitative Structure Activity Relationship (QSAR)-based protocols. However, such studies are typically conducted on different datasets, using different validation strategies, and different metrics. In this study, different methods were compared using one single standardized dataset obtained from ChEMBL, which is made available to the public, using standardized metrics (BEDROC and Matthews Correlation Coefficient). Specifically, the performance of Naïve Bayes, Random Forests, Support Vector Machines, Logistic Regression, and Deep Neural Networks was assessed using QSAR and proteochemometric (PCM) methods. All methods were validated using both a random split validation and a temporal validation, with the latter being a more realistic benchmark of expected prospective execution. Deep Neural Networks are the top performing classifiers, highlighting the added value of Deep Neural Networks over other more conventional methods. Moreover, the best method (‘DNN_PCM’) performed significantly better at almost one standard deviation higher than the mean performance. Furthermore, Multi-task and PCM implementations were shown to improve performance over single task Deep Neural Networks. Conversely, target prediction performed almost two standard deviations under the mean performance. Random Forests, Support Vector Machines, and Logistic Regression performed around mean performance. Finally, using an ensemble of DNNs, alongside additional tuning, enhanced the relative performance by another 27% (compared with unoptimized ‘DNN_PCM’). Here, a standardized set to test and evaluate different machine learning algorithms in the context of multi-task learning is offered by providing the data and the protocols. Graphical Abstract .
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- 2017
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11. In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor.
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Eelke B. Lenselink, Thijs Beuming, Corine van Veen, Arnault Massink, Woody Sherman, Herman W. T. van Vlijmen, and Adriaan P. IJzerman
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- 2016
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12. Relative Binding Free Energy Calculations Applied to Protein Homology Models.
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Daniel Cappel, Michelle Lynn Hall, Eelke B. Lenselink, Thijs Beuming, Jun Qi, James Bradner, and Woody Sherman
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- 2016
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13. Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening.
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Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Gerard J. P. van Westen
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- 2016
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14. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
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Eelke B. Lenselink, Julien Louvel, Anna F. Forti, Jacobus P. D. van Veldhoven, Henk de Vries, Thea Mulder-Krieger, Fiona M. McRobb, Ana Negri, Joseph Goose, Robert Abel, Herman W. T. van Vlijmen, Lingle Wang, Edward Harder, Woody Sherman, Adriaan P. IJzerman, and Thijs Beuming
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Chemistry ,QD1-999 - Published
- 2016
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15. Enhancing hit discovery in virtual screening through accurate calculation of absolute protein-ligand binding free energies
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Wei Chen, Di Cui, Steven V. Jerome, Mayako Michino, Eelke B. Lenselink, David Huggins, Alexandre Beautrait, Jeremie Vendome, Robert Abel, Richard A. Friesner, and Lingle Wang
- Abstract
In the hit identification stage of drug discovery, a diverse chemical space needs to be explored to identify initial hits. Contrary to empirical scoring functions, absolute protein-ligand binding free energy perturbation (ABFEP) provides a theoretically more rigorous and accurate description of protein-ligand binding thermodynamics and could in principle greatly improve the hit rates in virtual screening. In this work, we describe an implementation of an accurate and reliable ABFEP method in FEP+. We validated the ABFEP method on eight congeneric compound series binding to eight protein receptors including both neutral and charged ligands. For ligands with net charges, the alchemical ion approach is adopted to avoid artifacts in electrostatic potential energy calculations. The calculated binding free energies are highly correlated with experimental results with the weighted average of R2 of 0.55 for the entire dataset and an overall RMSE of 1.1 kcal/mol when protein reorganization effect upon ligand binding was accounted for. Through ABFEP calculations using apo versus holo protein structures, we demonstrated that the protein conformational and protonation state changes between the apo and holo proteins are the main physical factors contributing to the protein reorganization free energy manifested by the overestimation of raw ABFEP calculated binding free energies using the holo structures of the proteins. Furthermore, we performed ABFEP calculations in three virtual screening applications for hit enrichment. ABFEP greatly improves the hit rates as compared to docking scores or other methods like metadynamics. The highly accurate ABFEP results demonstrated in this work position it as a useful tool to improve the hit rates in virtual screening, thus facilitate hit discovery.
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- 2022
16. Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor.
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Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, and Adriaan P. IJzerman
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- 2014
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17. Construction of balanced, chemically dissimilar training, validation and test sets for machine learning on molecular datasets
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Giovanni A. Tricarico, Johan Hofmans, Eelke B. Lenselink, Miriam López Ramos, Marie-Pierre Dréanic, and Pieter F. W. Stouten
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When preparing training, validation and test sets for machine learning on molecular datasets, it is desirable to combine two requirements: 1) robustness, i.e. making a test set that is chemically dissimilar from the training set; 2) data balance, i.e. ensuring that the proportion of data points and the distribution of data labels (categorical) / data values (continuous) are as homogeneous as possible among the sets, for each individual property to model, while partitioning the overall set of compounds as required. Recent literature shows that meeting both these requirements simultaneously is sometimes very difficult. This is especially true for multi-task learning, but also for single-task learning if one aims to balance the distribution of data labels or values, too. In this work we present a method that resolves this issue by first carrying out a chemistry-guided clustering of the initial dataset to ensure the separation of chemical matter, and subsequently applying linear programming to select the lists of clusters that – once assembled into the final sets – result in the best possible data balance.
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- 2022
18. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation
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Gary Tresadern, Herman van Vlijmen, Jonathan S. Mason, Eelke B. Lenselink, Francesca Deflorian, Chris de Graaf, Laura Pérez-Benito, and Miles Congreve
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chemistry.chemical_classification ,010304 chemical physics ,Chemistry ,Hydrogen bond ,Drug discovery ,Globular protein ,Entropy ,General Chemical Engineering ,Binding energy ,General Chemistry ,Library and Information Sciences ,Ligands ,Ligand (biochemistry) ,01 natural sciences ,Receptors, G-Protein-Coupled ,0104 chemical sciences ,Computer Science Applications ,Free energy perturbation ,010404 medicinal & biomolecular chemistry ,Solvation shell ,Chemical physics ,0103 physical sciences ,Thermodynamics ,Protein Binding ,Protein ligand - Abstract
The computational prediction of relative binding free energies is a crucial goal for drug discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug target class. However, they present increased complexity to model compared to soluble globular proteins. Despite breakthroughs, experimental X-ray crystal and cryo-EM structures are challenging to attain, meaning computational models of the receptor and ligand binding mode are sometimes necessary. This leads to uncertainty in understanding ligand-protein binding induced changes such as, water positioning and displacement, side chain positioning, hydrogen bond networks, and the overall structure of the hydration shell around the ligand and protein. In other words, the very elements that define structure activity relationships (SARs) and are crucial for accurate binding free energy calculations are typically more uncertain for GPCRs. In this work we use free energy perturbation (FEP) to predict the relative binding free energies for ligands of two different GPCRs. We pinpoint the key aspects for success such as the important role of key water molecules, amino acid ionization states, and the benefit of equilibration with specific ligands. Initial calculations following typical FEP setup and execution protocols delivered no correlation with experiment, but we show how results are improved in a logical and systematic way. This approach gave, in the best cases, a coefficient of determination (R2) compared with experiment in the range of 0.6-0.9 and mean unsigned errors compared to experiment of 0.6-0.7 kcal/mol. We anticipate that our findings will be applicable to other difficult-to-model protein ligand data sets and be of wide interest for the community to continue improving FE binding energy predictions.
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- 2020
19. Synthesis and Pharmacological Evaluation of Triazolopyrimidinone Derivatives as Noncompetitive, Intracellular Antagonists for CC Chemokine Receptors 2 and 5
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Joseph Openy, Adriaan P. IJzerman, Burak Dogan, Ya-Yun Hsiao, Eelke B. Lenselink, Jacobus P. D. van Veldhoven, Natalia V. Ortiz Zacarías, Laura H. Heitman, and Lisa S den Hollander
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CCR2 ,Receptors, CCR5 ,Receptors, CCR2 ,animal diseases ,Antineoplastic Agents ,Bone Neoplasms ,Pharmacology ,Ligands ,01 natural sciences ,Article ,Radioligand Assay ,Structure-Activity Relationship ,03 medical and health sciences ,Chemokine receptor ,parasitic diseases ,Drug Discovery ,Tumor Cells, Cultured ,Humans ,Structure–activity relationship ,Binding site ,Receptor ,Cell Proliferation ,030304 developmental biology ,Osteosarcoma ,0303 health sciences ,Binding Sites ,Molecular Structure ,Chemistry ,hemic and immune systems ,Biological activity ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,Purines ,Molecular Medicine ,Intracellular ,Protein Binding - Abstract
CC chemokine receptors 2 (CCR2) and 5 (CCR5) are involved in many inflammatory diseases; however, most CCR2 and CCR5 clinical candidates have been unsuccessful. (Pre)clinical evidence suggests that dual CCR2/CCR5 inhibition might be more effective in the treatment of such multifactorial diseases. In this regard, the highly conserved intracellular binding site in chemokine receptors provides a new avenue for the design of multitarget ligands. In this study, we synthesized and evaluated the biological activity of a series of triazolopyrimidinone derivatives in CCR2 and CCR5. Radioligand binding assays first showed that they bind to the intracellular site of CCR2, and in combination with functional assays on CCR5, we explored structure−affinity/activity relationships in both receptors. Although most compounds were CCR2-selective, 39 and 43 inhibited β-arrestin recruitment in CCR5 with high potency. Moreover, these compounds displayed an insurmountable mechanism of inhibition in both receptors, which holds promise for improved efficacy in inflammatory diseases.
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- 2019
20. Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors
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Sebastian H. Grimm, Eelke B. Lenselink, Adriaan W. Tuin, Constant A. A. van Boeckel, Adrianus M. C. H. van den Nieuwendijk, Ruud H. Wijdeven, Jordi F. Keijzer, Mario van der Stelt, Herman S. Overkleeft, Jacques Neefjes, Nora Liu, Gerard J. P. van Westen, and Berend Gagestein
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Fms-like tyrosine kinase 3 (FLT3) ,Indoles ,Acutemyeloidleukemia(AML) ,Clinical Biochemistry ,Pharmaceutical Science ,medicine.disease_cause ,01 natural sciences ,Biochemistry ,Structure-Activity Relationship ,hemic and lymphatic diseases ,Drug Discovery ,Acute myeloid leukemia (AML) ,medicine ,Humans ,Structure–activity relationship ,Receptor ,Protein Kinase Inhibitors ,Fms-liketyrosinekinase3(FLT3) ,Molecular Biology ,Aza Compounds ,Mutation ,Binding Sites ,Molecular Structure ,Inhibitors ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Cancer ,Myeloid leukemia ,Drug resistant mutants ,medicine.disease ,0104 chemical sciences ,Molecular Docking Simulation ,010404 medicinal & biomolecular chemistry ,fms-Like Tyrosine Kinase 3 ,H-89analogs ,Tyrosine Kinase 3 ,Cancer research ,H-89 analogs ,Molecular Medicine ,Matched molecular pair analysis ,Protein Binding - Abstract
Acute myeloid leukemia (AML) is characterized by fast progression and low survival rates, in which Fms-like tyrosine kinase 3 (FLT3) receptor mutations have been identified as a driver mutation in cancer progression in a subgroup of AML patients. Clinical trials have shown emergence of drug resistant mutants, emphasizing the ongoing need for new chemical matter to enable the treatment of this disease. Here, we present the discovery and topological structure-activity relationship (SAR) study of analogs of isoquinolinesulfonamide H-89, a well-known PKA inhibitor, as FLT3 inhibitors. Surprisingly, we found that the SAR was not consistent with the observed binding mode of H-89 in PKA. Matched molecular pair analysis resulted in the identification of highly active sub-nanomolar azaindoles as novel FLT3-inhibitors. Structure based modelling using the FLT3 crystal structure suggested an alternative, flipped binding orientation of the new inhibitors.
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- 2019
21. Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis
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Tim van den Hooven, Joost A. P. M. Wijnakker, Tjeerd Barf, Herman S. Overkleeft, Hans den Dulk, Rob Ruijtenbeek, Tom van der Wel, Eelke B. Lenselink, Allard Kaptein, Gerard J. P. van Westen, Bogdan I. Florea, Nienke M. Prins, Mario van der Stelt, and Riet Hilhorst
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0301 basic medicine ,Neutrophils ,Science ,Cellular differentiation ,General Physics and Astronomy ,Kinases ,Article ,Chemical genetics ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,03 medical and health sciences ,0302 clinical medicine ,Phagocytosis ,Fluorescence Resonance Energy Transfer ,Humans ,Syk Kinase ,CRISPR ,lcsh:Science ,Sensors and probes ,Fluorescent Dyes ,Gene Editing ,Multidisciplinary ,Drug discovery ,Chemistry ,Kinase ,Cas9 ,Macrophages ,Cell Differentiation ,General Chemistry ,Protein-Tyrosine Kinases ,Cell biology ,030104 developmental biology ,Proto-Oncogene Proteins c-fes ,030220 oncology & carcinogenesis ,Mutation ,lcsh:Q ,ATP-Binding Cassette Transporters ,CRISPR-Cas Systems ,Signal transduction ,Chemical tools ,Tyrosine kinase ,Signal Transduction - Abstract
Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine residue into cysteine at the DFG-1 position in the ATP-binding pocket, we sensitize the non-receptor tyrosine kinase FES towards covalent labeling by a complementary fluorescent chemical probe. This mutation is introduced in the endogenous FES gene of HL-60 cells using CRISPR/Cas9 gene editing. Leveraging the temporal and acute control offered by our strategy, we show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis via SYK kinase activation. This chemical genetics strategy holds promise as a target validation method for kinases., Chemical tools to monitor drug-target engagement of endogenous enzymes are essential for preclinical target validation. Here, the authors present a chemical genetics strategy to study target engagement of endogenous kinases, achieving specific labeling and inactivation of FES kinase to provide insights into FES’ role in neutrophil phagocytosis.
- Published
- 2020
22. Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors
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Marina Gorostiola González, Gerard J. P. van Westen, Brandon J. Bongers, Willem Jespers, Herman van Vlijmen, Rongfang Liu, Adriaan P. IJzerman, Jesper E. van Engelen, Lindsey Burggraaff, Eelke B. Lenselink, and Holger H. Hoos
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Polypharmacology ,General Chemical Engineering ,Antineoplastic Agents ,Context (language use) ,P70-S6 Kinase 1 ,Computational biology ,Library and Information Sciences ,01 natural sciences ,Article ,PAK1 ,0103 physical sciences ,Protein Kinase Inhibitors ,Virtual screening ,010304 chemical physics ,Chemistry ,Kinase ,Proto-Oncogene Proteins c-ret ,Läkemedelskemi ,General Chemistry ,0104 chemical sciences ,Computer Science Applications ,010404 medicinal & biomolecular chemistry ,Active compound ,Drug Design ,Structure based ,Medicinal Chemistry ,Proto-oncogene tyrosine-protein kinase Src - Abstract
Kinases are frequently studied in the context of anticancer drugs. Their involvement in cell responses, such as proliferation, differentiation, and apoptosis, makes them interesting subjects in multitarget drug design. In this study, a workflow is presented that models the bioactivity spectra for two panels of kinases: (1) inhibition of RET, BRAF, SRC, and S6K, while avoiding inhibition of MKNK1, TTK, ERK8, PDK1, and PAK3, and (2) inhibition of AURKA, PAK1, FGFR1, and LKB1, while avoiding inhibition of PAK3, TAK1, and PIK3CA. Both statistical and structure-based models were included, which were thoroughly benchmarked and optimized. A virtual screening was performed to test the workflow for one of the main targets, RET kinase. This resulted in 5 novel and chemically dissimilar RET inhibitors with remaining RET activity of 50 value of 5.1 for the most active compound. The experimental validation of inhibitors for RET strongly indicates that the multitarget workflow is able to detect novel inhibitors for kinases, and hence, this workflow can potentially be applied in polypharmacology modeling. We conclude that this approach can identify new chemical matter for existing targets. Moreover, this workflow can easily be applied to other targets as well.
- Published
- 2020
23. Pyrrolone Derivatives as Intracellular Allosteric Modulators for Chemokine Receptors: Selective and Dual-Targeting Inhibitors of CC Chemokine Receptors 1 and 2
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Annelien J.M. Zweemer, Adriaan P. IJzerman, Roy M. Kreekel, Eelke B. Lenselink, Jacobus P. D. van Veldhoven, Natalia V. Ortiz Zacarías, Wijnand J. C. van der Velden, Laura Portner, Laura H. Heitman, Salviana Ullo, Eric van Spronsen, Kenny Oenema, and Margo Veenhuizen
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0301 basic medicine ,CCR1 ,CCR2 ,Protein Conformation ,Receptors, CCR2 ,Allosteric regulation ,Intracellular Space ,Receptors, CCR1 ,Ligands ,Article ,Structure-Activity Relationship ,03 medical and health sciences ,Chemokine receptor ,Allosteric Regulation ,Drug Discovery ,Radioligand ,Humans ,Pyrroles ,Binding site ,Chemistry ,Molecular Docking Simulation ,030104 developmental biology ,Biochemistry ,Molecular Medicine ,CC chemokine receptors ,Intracellular - Abstract
The recent crystal structures of CC chemokine receptors 2 and 9 (CCR2 and CCR9) have provided structural evidence for an allosteric, intracellular binding site. The high conservation of residues involved in this site suggests its presence in most chemokine receptors, including the close homologue CCR1. By using [H-3]CCR2-RA-[R], a high-affinity, CCR2 intracellular ligand, we report an intracellular binding site in CCR1, where this radioligand also binds with high affinity. In addition, we report the synthesis and biological characterization of a series of pyrrolone derivatives for CCR1 and CCR2, which allowed us to identify several high-affinity intracellular ligands, including selective and potential multitarget antagonists. Evaluation of selected compounds in a functional [S-35]GTP gamma S assay revealed that they act as inverse agonists in CCR1, providing a new manner of pharmacological modulation. Thus, this intracellular binding site enables the design of selective and multitarget inhibitors as a novel therapeutic approach.
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- 2018
24. Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis via SYK activation
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Nienke M. Prins, Rob Ruijtenbeek, Bogdan I. Florea, Joost A. P. M. Wijnakker, Mario van der Stelt, Hans den Dulk, Eelke B. Lenselink, Allard Kaptein, Tom van der Wel, Riet Hilhorst, Gerard J. P. van Westen, Tim van den Hooven, Tjeerd Barf, and Herman S. Overkleeft
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Serine ,Immune system ,Chemistry ,Kinase ,Regulator ,Syk ,Chemical genetics ,Tyrosine kinase ,Small molecule ,Cell biology - Abstract
Chemical tools and methods that report on target engagement of endogenously expressed protein kinases by small molecules in human cells are highly desirable. Here, we describe a chemical genetics strategy that allows the study of non-receptor tyrosine kinase FES, a promising therapeutic target for cancer and immune disorders. Precise gene editing was used in combination with a rationally designed, complementary fluorescent probe to visualize endogenous FES kinase in HL-60 cells. We replaced a single oxygen atom by a sulphur in a serine residue at the DFG-1 position of the ATP-binding pocket in an endogenously expressed kinase, thereby sensitizing the engineered protein towards covalent labeling and inactivation by a fluorescent probe. The temporal control offered by this strategy allows acute inactivation of FES activity both during myeloid differentiation and in terminally differentiated neutrophils. Our results show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis by activation of SYK kinase, a central regulator of immune function in neutrophils. This strategy holds promise as a target validation method for kinases.
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- 2019
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25. Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling.
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Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender 0002, and Therese E. Malliavin
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- 2015
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26. Proteochemometric modeling in a Bayesian framework.
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Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender 0002, and Thérèse E. Malliavin
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- 2014
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27. Development of Covalent Ligands for G Protein-Coupled Receptors: A Case for the Human Adenosine A3 Receptor
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Daan van der Es, Adriaan P. IJzerman, Jelle Offringa, Xue Yang, Laura H. Heitman, Eelke B. Lenselink, Jacobus P. D. van Veldhoven, and Boaz J. Kuiper
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0303 health sciences ,Chemistry ,Stereochemistry ,Covalent Interaction ,Adenosine A3 receptor ,01 natural sciences ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,03 medical and health sciences ,Covalent bond ,Drug Discovery ,Molecular Medicine ,Structure–activity relationship ,Binding site ,Receptor ,Linker ,030304 developmental biology ,G protein-coupled receptor - Abstract
The development of covalent ligands for G protein-coupled receptors (GPCRs) is not a trivial process. Here, we report a streamlined workflow thereto from synthesis to validation, exemplified by the discovery of a covalent antagonist for the human adenosine A3 receptor (hA3AR). Based on the 1H,3H-pyrido[2,1-f]purine-2,4-dione scaffold, a series of ligands bearing a fluorosulfonyl warhead and a varying linker was synthesized. This series was subjected to an affinity screen, revealing compound 17b as the most potent antagonist. In addition, a nonreactive methylsulfonyl derivative 19 was developed as a reversible control compound. A series of assays, comprising time-dependent affinity determination, washout experiments, and [35S]GTPγS binding assays, then validated 17b as the covalent antagonist. A combined in silico hA3AR-homology model and site-directed mutagenesis study was performed to demonstrate that amino acid residue Y2657.36 was the unique anchor point of the covalent interaction. This workflow might be applied to other GPCRs to guide the discovery of covalent ligands.
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- 2019
28. Development of Covalent Ligands for G Protein-Coupled Receptors: A Case for the Human Adenosine A
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Xue, Yang, Jacobus P D, van Veldhoven, Jelle, Offringa, Boaz J, Kuiper, Eelke B, Lenselink, Laura H, Heitman, Daan, van der Es, and Adriaan P, IJzerman
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Structure-Activity Relationship ,Binding Sites ,Cricetulus ,Guanosine 5'-O-(3-Thiotriphosphate) ,Receptor, Adenosine A3 ,Adenosine A3 Receptor Antagonists ,Animals ,Humans ,CHO Cells ,Ligands - Abstract
[Image: see text] The development of covalent ligands for G protein-coupled receptors (GPCRs) is not a trivial process. Here, we report a streamlined workflow thereto from synthesis to validation, exemplified by the discovery of a covalent antagonist for the human adenosine A(3) receptor (hA(3)AR). Based on the 1H,3H-pyrido[2,1-f]purine-2,4-dione scaffold, a series of ligands bearing a fluorosulfonyl warhead and a varying linker was synthesized. This series was subjected to an affinity screen, revealing compound 17b as the most potent antagonist. In addition, a nonreactive methylsulfonyl derivative 19 was developed as a reversible control compound. A series of assays, comprising time-dependent affinity determination, washout experiments, and [(35)S]GTPγS binding assays, then validated 17b as the covalent antagonist. A combined in silico hA(3)AR-homology model and site-directed mutagenesis study was performed to demonstrate that amino acid residue Y265(7.36) was the unique anchor point of the covalent interaction. This workflow might be applied to other GPCRs to guide the discovery of covalent ligands.
- Published
- 2019
29. In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor
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Adriaan P. IJzerman, Thijs Beuming, Eelke B. Lenselink, Woody Sherman, Herman W. T. van Vlijmen, Arnault Massink, and Corine van Veen
- Subjects
Virtual screening ,0301 basic medicine ,Denticity ,Adenosine A2 Receptor Agonists ,Databases, Factual ,Receptor, Adenosine A2A ,Stereochemistry ,Explicit water ,Drug Evaluation, Preclinical ,Adenosine A2A receptor ,Ligands ,01 natural sciences ,Article ,Radioligand Assay ,Structure-Activity Relationship ,03 medical and health sciences ,Drug Discovery ,Radioligand ,Humans ,Molecule ,Computer Simulation ,Novel ligand ,Physical and Theoretical Chemistry ,Receptor ,Binding Sites ,Ligand efficiency ,Molecular Structure ,Chemistry ,Water ,Combinatorial chemistry ,Adenosine A2 Receptor Antagonists ,0104 chemical sciences ,Computer Science Applications ,Molecular Docking Simulation ,010404 medicinal & biomolecular chemistry ,HEK293 Cells ,030104 developmental biology ,Structure based ,Diverse chemical space - Abstract
In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand binding site to prospectively screen over 2.5 million drug-like and lead-like compounds from the commercially available eMolecules database in search of novel binders to the adenosine A2A receptor (A2AAR). A total of seventy-one compounds were selected for purchase and biochemical assaying based on high ligand efficiency and high novelty (Tanimoto coefficient ≤0.25 to any A2AAR tested compound). These molecules were then tested for their affinity to the adenosine A2A receptor in a radioligand binding assay. We identified two hits that fulfilled the criterion of ~50 % radioligand displacement at a concentration of 10 μM. Next we selected an additional eight novel molecules that were predicted to make a bidentate interaction with Asn2536.55, a key interacting residue in the binding pocket of the A2AAR. None of these eight molecules were found to be active. Based on these results we discuss the advantages of structure-based methods and the challenges associated with finding chemically novel molecules for well-explored targets. Electronic supplementary material The online version of this article (doi:10.1007/s10822-016-9963-7) contains supplementary material, which is available to authorized users.
- Published
- 2016
30. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
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Lingle Wang, Fiona M. McRobb, Joseph E. Goose, Edward Harder, Robert Abel, Thijs Beuming, Eelke B. Lenselink, Jacobus P. D. van Veldhoven, Julien Louvel, Henk de Vries, Anna F. Forti, Thea Mulder-Krieger, Andrea Negri, Herman W. T. van Vlijmen, Adriaan P. IJzerman, and Woody Sherman
- Subjects
0301 basic medicine ,Virtual screening ,010304 chemical physics ,Chemistry ,General Chemical Engineering ,General Chemistry ,01 natural sciences ,Article ,Free energy perturbation ,lcsh:Chemistry ,03 medical and health sciences ,030104 developmental biology ,lcsh:QD1-999 ,Computational chemistry ,0103 physical sciences ,Free energies ,Lipid bilayer ,Selectivity ,Receptor ,G protein-coupled receptor ,Binding affinities - Abstract
The rapid growth of structural information for G-protein-coupled receptors (GPCRs) has led to a greater understanding of their structure, function, selectivity, and ligand binding. Although novel ligands have been identified using methods such as virtual screening, computationally driven lead optimization has been possible only in isolated cases because of challenges associated with predicting binding free energies for related compounds. Here, we provide a systematic characterization of the performance of free-energy perturbation (FEP) calculations to predict relative binding free energies of congeneric ligands binding to GPCR targets using a consistent protocol and no adjustable parameters. Using the FEP+ package, first we validated the protocol, which includes a full lipid bilayer and explicit solvent, by predicting the binding affinity for a total of 45 different ligands across four different GPCRs (adenosine A2AAR, β1 adrenergic, CXCR4 chemokine, and δ opioid receptors). Comparison with experimental binding affinity measurements revealed a highly predictive ranking correlation (average spearman ρ = 0.55) and low root-mean-square error (0.80 kcal/mol). Next, we applied FEP+ in a prospective project, where we predicted the affinity of novel, potent adenosine A2A receptor (A2AR) antagonists. Four novel compounds were synthesized and tested in a radioligand displacement assay, yielding affinity values in the nanomolar range. The affinity of two out of the four novel ligands (plus three previously reported compounds) was correctly predicted (within 1 kcal/mol), including one compound with approximately a tenfold increase in affinity compared to the starting compound. Detailed analyses of the simulations underlying the predictions provided insights into the structural basis for the two cases where the affinity was overpredicted. Taken together, these results establish a protocol for systematically applying FEP+ to GPCRs and provide guidelines for identifying potent molecules in drug discovery lead optimization projects.
- Published
- 2016
31. 5′-Substituted Amiloride Derivatives as Allosteric Modulators Binding in the Sodium Ion Pocket of the Adenosine A2A Receptor
- Author
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Berend J. H. Huisman, Marie Ranson, Dong Guo, Ilze Adlere, Corine van Veen, Arnault Massink, Eelke B. Lenselink, Gabrielle S. Dijksteel, Michael J. Kelso, Hayden Matthews, Benjamin J. Buckley, Adriaan P. IJzerman, and Julien Louvel
- Subjects
0301 basic medicine ,Receptor, Adenosine A2A ,Stereochemistry ,Sodium ,Mutant ,Allosteric regulation ,chemistry.chemical_element ,Adenosine A2A receptor ,Amiloride ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,Allosteric Regulation ,Drug Discovery ,Radioligand ,medicine ,Humans ,Receptor ,G protein-coupled receptor ,Molecular Structure ,Chemistry ,Adenosine A2 Receptor Antagonists ,3. Good health ,Molecular Docking Simulation ,030104 developmental biology ,Biochemistry ,030220 oncology & carcinogenesis ,Molecular Medicine ,Allosteric Site ,medicine.drug - Abstract
The sodium ion site is an allosteric site conserved among many G protein-coupled receptors (GPCRs). Amiloride 1 and 5-(N,N-hexamethylene)amiloride 2 (HMA) supposedly bind in this sodium ion site and can influence orthosteric ligand binding. The availability of a high-resolution X-ray crystal structure of the human adenosine A2A receptor (hA2AAR), in which the allosteric sodium ion site was elucidated, makes it an appropriate model receptor for investigating the allosteric site. In this study, we report the synthesis and evaluation of novel 5'-substituted amiloride derivatives as hA2AAR allosteric antagonists. The potency of the amiloride derivatives was assessed by their ability to displace orthosteric radioligand [(3)H]4-(2-((7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a]-[1,3,5]triazin-5-yl)amino)ethyl)phenol ([(3)H]ZM-241,385) from both the wild-type and sodium ion site W246A mutant hA2AAR. 4-Ethoxyphenethyl-substituted amiloride 12l was found to be more potent than both amiloride and HMA, and the shift in potency between the wild-type and mutated receptor confirmed its likely binding to the sodium ion site.
- Published
- 2016
32. Application of portfolio optimization to drug discovery
- Author
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Michael Emmerich, Eelke B. Lenselink, Adriaan P. IJzerman, André H. Deutz, Iryna Yevseyeva, and Alice de Vries
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Mathematical optimization ,Decision support system ,Information Systems and Management ,Computer science ,education ,02 engineering and technology ,Measure (mathematics) ,Multi-objective optimization ,Theoretical Computer Science ,Financial management ,Set (abstract data type) ,Artificial Intelligence ,0202 electrical engineering, electronic engineering, information engineering ,Selection (genetic algorithm) ,Rate of return ,Multicriteria optimization ,business.industry ,Covariance matrix ,Drug discovery ,05 social sciences ,050301 education ,Computer Science Applications ,Decision support ,Control and Systems Engineering ,Portfolio ,Portfolio approach ,020201 artificial intelligence & image processing ,Portfolio optimization ,business ,0503 education ,Software - Abstract
In this work, a problem of selecting a subset of molecules, which are potential lead candidates for drug discovery, is considered. Such molecule subset selection problem is formulated as a portfolio optimization, well known and studied in financial management. The financial return, more precisely the return rate, is interpreted as return rate from a potential lead and calculated as a product of gain and probability of success (probability that a selected molecule becomes a lead), which is related to performance of the molecule, in particular, its (bio-)activity. The risk is associated with not finding active molecules and is related to the level of diversity of the molecules selected in portfolio. It is due to potential of some molecules to contribute to the diversity of the set of molecules selected in portfolio and hence decreasing risk of portfolio as a whole. Even though such molecules considered in isolation look inefficient, they are located in sparsely sampled regions of chemical space and are different from more promising molecules. One way of computing diversity of a set is associated with a covariance matrix, and here it is represented by the Solow-Polasky measure. Several formulations of molecule portfolio optimization are considered taking into account the limited budget provided for buying molecules and the fixed size of the portfolio. The proposed approach is tested in experimental settings for three molecules datasets using exact and/or evolutionary approaches. The results obtained for these datasets look promising and encouraging for application of the proposed portfolio-based approach for molecule subset selection in real settings.Graphical abstract
- Published
- 2018
33. Intracellular Receptor Modulation: Novel Approach to Target GPCRs
- Author
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Laura H. Heitman, Eelke B. Lenselink, Adriaan P. IJzerman, Tracy M. Handel, and Natalia V. Ortiz Zacarías
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0301 basic medicine ,Models, Molecular ,G protein ,Protein Conformation ,Allosteric regulation ,Toxicology ,Ligands ,Receptors, G-Protein-Coupled ,Small Molecule Libraries ,03 medical and health sciences ,Chemokine receptor ,Drug Delivery Systems ,Allosteric Regulation ,G protein-coupled receptors ,Intracellular receptor ,Humans ,Molecular Targeted Therapy ,Binding site ,G protein-coupled receptor ,Pharmacology ,allosteric modulation ,Chemistry ,Small molecule ,antagonism ,Cell biology ,small molecules ,030104 developmental biology ,Drug Design ,Intracellular ,Allosteric Site ,Signal Transduction ,intracellular binding site - Abstract
Recent crystal structures of multiple G protein-coupled receptors (GPCRs) have revealed a highly conserved intracellular pocket that can be used to modulate these receptors from the inside. This novel intracellular site partially overlaps with the G protein and β-arrestin binding site, providing a new manner of pharmacological intervention. Here we provide an update of the architecture and function of the intracellular region of GPCRs, until now portrayed as the signaling domain. We review the available evidence on the presence of intracellular binding sites among chemokine receptors and other class A GPCRs, as well as different strategies to target it, including small molecules, pepducins, and nanobodies. Finally, the potential advantages of intracellular (allosteric) ligands over orthosteric ligands are also discussed.
- Published
- 2018
34. Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome–Inhibitor Interaction Landscapes
- Author
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Mario van der Stelt, Ruud H. Wijdeven, Sebastian H. Grimm, Eelke B. Lenselink, Gerard J. P. van Westen, Constant A. A. van Boeckel, Jacques Neefjes, and Antonius P A Janssen
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Models, Molecular ,Protein family ,Computer science ,Protein Conformation ,General Chemical Engineering ,Library and Information Sciences ,Machine learning ,computer.software_genre ,01 natural sciences ,Article ,Machine Learning ,0103 physical sciences ,Drug Discovery ,Kinome ,Independent data ,Protein Kinase Inhibitors ,010304 chemical physics ,Drug discovery ,business.industry ,Kinase Family ,General Chemistry ,computer.file_format ,0104 chemical sciences ,Computer Science Applications ,Visualization ,010404 medicinal & biomolecular chemistry ,fms-Like Tyrosine Kinase 3 ,Tyrosine Kinase 3 ,Artificial intelligence ,Executable ,business ,computer ,Protein Kinases ,Protein Binding - Abstract
The interpretation of high-dimensional structure-activity data sets in drug discovery to predict ligand-protein interaction landscapes is a challenging task. Here we present Drug Discovery Maps (DDM), a machine learning model that maps the activity profile of compounds across an entire protein family, as illustrated here for the kinase family. DDM is based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm to generate a visualization of molecular and biological similarity. DDM maps chemical and target space and predicts the activities of novel kinase inhibitors across the kinome. The model was validated using independent data sets and in a prospective experimental setting, where DDM predicted new inhibitors for FMS-like tyrosine kinase 3 (FLT3), a therapeutic target for the treatment of acute myeloid leukemia. Compounds were resynthesized, yielding highly potent, cellularly active FLT3 inhibitors. Biochemical assays confirmed most of the predicted off-targets. DDM is further unique in that it is completely open-source and available as a ready-to-use executable to facilitate broad and easy adoption.
- Published
- 2018
35. Structure-Affinity Relationships and Structure-Kinetic Relationships of 1,2-Diarylimidazol-4-carboxamide Derivatives as Human Cannabinoid 1 Receptor Antagonists
- Author
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Robert J. Sheppard, Peter Schell, Eelke B. Lenselink, Leifeng Cheng, Laura H. Heitman, Adriaan P. IJzerman, Henk de Vries, Maria J. Petersson, Roine I. Olsson, Sara Pahlén, Michael J. Waring, Lizi Xia, and Julien Louvel
- Subjects
0301 basic medicine ,Models, Molecular ,Stereochemistry ,medicine.drug_class ,medicine.medical_treatment ,Carboxamide ,CHO Cells ,Article ,03 medical and health sciences ,Structure-Activity Relationship ,0302 clinical medicine ,Cricetulus ,Receptor, Cannabinoid, CB1 ,Drug Discovery ,Radioligand ,medicine ,Structure–activity relationship ,Animals ,Humans ,Receptor ,Chemistry ,Drug discovery ,Ligand binding assay ,Imidazoles ,Receptor–ligand kinetics ,Molecular Docking Simulation ,Kinetics ,030104 developmental biology ,HEK293 Cells ,Molecular Medicine ,Cannabinoid ,030217 neurology & neurosurgery - Abstract
We report on the synthesis and biological evaluation of a series of 1,2-diarylimidazol-4-carboxamide derivatives developed as CB1 receptor antagonists. These were evaluated in a radioligand displacement binding assay, a [35S]GTPγS binding assay, and in a competition association assay that enables the relatively fast kinetic screening of multiple compounds. The compounds show high affinities and a diverse range of kinetic profiles at the CB1 receptor and their structure–kinetic relationships (SKRs) were established. Using the recently resolved hCB1 receptor crystal structures, we also performed a modeling study that sheds light on the crucial interactions for both the affinity and dissociation kinetics of this family of ligands. We provide evidence that, next to affinity, additional knowledge of binding kinetics is useful for selecting new hCB1 receptor antagonists in the early phases of drug discovery.
- Published
- 2017
36. Structure-kinetics relationships of Capadenoson derivatives as adenosine A 1 receptor agonists
- Author
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Laura H. Heitman, Adriaan P. IJzerman, Julien Louvel, Tamara A. M. Mocking, Marjolein Soethoudt, Thea Mulder-Krieger, Eelke B. Lenselink, and Dong Guo
- Subjects
Structure-affinity relationships ,Models, Molecular ,Stereochemistry ,Kinetics ,Aminopyridines ,Extracellular loops ,Structure-Activity Relationship ,Adenosine A1 receptor ,Capadenoson ,Drug Discovery ,Humans ,Homology modeling ,Structure-kinetics relationships ,Pharmacology ,Ligand efficiency ,Dose-Response Relationship, Drug ,Molecular Structure ,Receptor, Adenosine A1 ,Chemistry ,Drug candidate ,Residence time ,Organic Chemistry ,General Medicine ,Receptor–ligand kinetics ,Adenosine A1 Receptor Agonists ,Thiazoles ,Adenosine A(1) receptor ,Dissociation kinetics - Abstract
We report the synthesis and biological evaluation of new derivatives of Capadenoson, a former drug candidate that was previously advanced to phase IIa clinical trials. 19 of the 20 ligands show an affinity below 100 nM at the human adenosine A1 receptor (hA1AR) and display a wide range of residence times at this target (from approx. 5 min (compound 10) up to 132 min (compound 5)). Structure-affinity and structure-kinetics relationships were established, and computational studies of a homology model of the hA1AR revealed crucial interactions for both the affinity and dissociation kinetics of this family of ligands. These results were also combined with global metrics (Ligand Efficiency, cLogP), showing the importance of binding kinetics as an additional way to better select a drug candidate amongst seemingly similar leads.
- Published
- 2015
37. Sodium Ion Binding Pocket Mutations and Adenosine A2AReceptor Function
- Author
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Natalia V. Ortiz Zacarías, Lizi Xia, Raymond C. Stevens, Eelke B. Lenselink, Adriaan P. IJzerman, Laura H. Heitman, Vsevolod Katritch, Hugo Gutiérrez-de-Terán, and Arnault Massink
- Subjects
Receptor, Adenosine A2A ,Sodium ,Allosteric regulation ,Adenosine A2A receptor ,chemistry.chemical_element ,Crystallography, X-Ray ,Protein Structure, Secondary ,Allosteric Regulation ,medicine ,Humans ,Binding site ,Receptor ,Pharmacology ,Binding Sites ,Dose-Response Relationship, Drug ,Ligand (biochemistry) ,Amiloride ,HEK293 Cells ,chemistry ,Biochemistry ,Mutation ,Biophysics ,Molecular Medicine ,Erratum ,Sodium ion binding ,medicine.drug - Abstract
Recently we identified a sodium ion binding pocket in a high-resolution structure of the human adenosine A2A receptor. In the present study we explored this binding site through site-directed mutagenesis and molecular dynamics simulations. Amino acids in the pocket were mutated to alanine, and their influence on agonist and antagonist affinity, allosterism by sodium ions and amilorides, and receptor functionality was explored. Mutation of the polar residues in the Na(+) pocket were shown to either abrogate (D52A(2.50) and N284A(7.49)) or reduce (S91A(3.39), W246A(6.48), and N280A(7.45)) the negative allosteric effect of sodium ions on agonist binding. Mutations D52A(2.50) and N284A(7.49) completely abolished receptor signaling, whereas mutations S91A(3.39) and N280A(7.45) elevated basal activity and mutations S91A(3.39), W246A(6.48), and N280A(7.45) decreased agonist-stimulated receptor signaling. In molecular dynamics simulations D52A(2.50) directly affected the mobility of sodium ions, which readily migrated to another pocket formed by Glu13(1.39) and His278(7.43). The D52A(2.50) mutation also decreased the potency of amiloride with respect to ligand displacement but did not change orthosteric ligand affinity. In contrast, W246A(6.48) increased some of the allosteric effects of sodium ions and amiloride, whereas orthosteric ligand binding was decreased. These new findings suggest that the sodium ion in the allosteric binding pocket not only impacts ligand affinity but also plays a vital role in receptor signaling. Because the sodium ion binding pocket is highly conserved in other class A G protein-coupled receptors, our findings may have a general relevance for these receptors and may guide the design of novel synthetic allosteric modulators or bitopic ligands.
- Published
- 2014
38. Structure-Affinity Relationships and Structure-Kinetics Relationships of Pyrido[2,1-f]purine-2,4-dione Derivatives as Human Adenosine A(3) Receptor Antagonists
- Author
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Eelke B. Lenselink, Jacobus P. D. van Veldhoven, Tirsa T. van Duijl, Laura H. Heitman, Adriaan P. IJzerman, Boaz J. Kuiper, Ellen Paasman, Lizi Xia, and Wessel A.C. Burger
- Subjects
0301 basic medicine ,Purine ,Stereochemistry ,Kinetics ,Adenosine A3 Receptor Antagonists ,CHO Cells ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Cricetulus ,Drug Discovery ,Animals ,Humans ,Receptor ,Drug discovery ,Chemistry ,Receptor, Adenosine A3 ,Adenosine A3 receptor ,Affinities ,Receptor–ligand kinetics ,Molecular Docking Simulation ,030104 developmental biology ,Biochemistry ,Purines ,Molecular Medicine - Abstract
We expanded on a series of pyrido[2,1-f]purine-2,4-dione derivatives as human adenosine A3 receptor (hA3R) antagonists to determine their kinetic profiles and affinities. Many compounds showed high affinities and a diverse range of kinetic profiles. We found hA3R antagonists with very short residence time (RT) at the receptor (2.2 min for 5) and much longer RTs (e.g., 376 min for 27 or 391 min for 31). Two representative antagonists (5 and 27) were tested in [35S]GTPγS binding assays, and their RTs appeared correlated to their (in)surmountable antagonism. From a kon-koff-KD kinetic map, we divided the antagonists into three subgroups, providing a possible direction for the further development of hA3R antagonists. Additionally, we performed a computational modeling study that sheds light on the crucial receptor interactions, dictating the compounds' binding kinetics. Knowledge of target binding kinetics appears useful for developing and triaging new hA3R antagonists in the early phase of drug discovery.
- Published
- 2017
39. Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set
- Author
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Adriaan P. IJzerman, Brandon J. Bongers, Eelke B. Lenselink, Wojtek Kowalczyk, Gerard J. P. van Westen, Niels ten Dijke, George Papadatos, and Herman W. T. van Vlijmen
- Subjects
0301 basic medicine ,Quantitative structure–activity relationship ,Computer science ,ChEMBL ,Multi-task learning ,Context (language use) ,Library and Information Sciences ,Machine learning ,computer.software_genre ,01 natural sciences ,Standard deviation ,lcsh:Chemistry ,03 medical and health sciences ,Naive Bayes classifier ,chemistry.chemical_compound ,Deep neural networks ,Chemogenomics ,Physical and Theoretical Chemistry ,030304 developmental biology ,0303 health sciences ,lcsh:T58.5-58.64 ,lcsh:Information technology ,QSAR ,business.industry ,Cheminformatics ,Matthews correlation coefficient ,chEMBL ,Computer Graphics and Computer-Aided Design ,Computer Science Applications ,0104 chemical sciences ,Random forest ,Support vector machine ,010404 medicinal & biomolecular chemistry ,030104 developmental biology ,lcsh:QD1-999 ,chemistry ,Benchmark (computing) ,Data mining ,Artificial intelligence ,business ,computer ,Proteochemometrics ,Research Article - Abstract
The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multitude of different methods have been reported and evaluated, such as target fishing, nearest neighbor similarity-based methods, and Quantitative Structure Activity Relationship (QSAR)-based protocols. However, such studies are typically conducted on different datasets, using different validation strategies, and different metrics. In this study, different methods were compared using one single standardized dataset obtained from ChEMBL, which is made available to the public, using standardized metrics (BEDROC and Matthews Correlation Coefficient). Specifically, the performance of Naïve Bayes, Random Forests, Support Vector Machines, Logistic Regression, and Deep Neural Networks was assessed using QSAR and proteochemometric (PCM) methods. All methods were validated using both a random split validation and a temporal validation, with the latter being a more realistic benchmark of expected prospective execution. Deep Neural Networks are the top performing classifiers, highlighting the added value of Deep Neural Networks over other more conventional methods. Moreover, the best method (‘DNN_PCM’) performed significantly better at almost one standard deviation higher than the mean performance. Furthermore, Multi-task and PCM implementations were shown to improve performance over single task Deep Neural Networks. Conversely, target prediction performed almost two standard deviations under the mean performance. Random Forests, Support Vector Machines, and Logistic Regression performed around mean performance. Finally, using an ensemble of DNNs, alongside additional tuning, enhanced the relative performance by another 27% (compared with unoptimized ‘DNN_PCM’). Here, a standardized set to test and evaluate different machine learning algorithms in the context of multi-task learning is offered by providing the data and the protocols.Graphical Abstract. Electronic supplementary material The online version of this article (doi:10.1186/s13321-017-0232-0) contains supplementary material, which is available to authorized users.
- Published
- 2017
40. Synthesis and evaluation of N-substituted 2-amino-4,5-diarylpyrimidines as selective adenosine A(1) receptor antagonists
- Author
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Henk de Vries, Adriaan P. IJzerman, Georgios Alachouzos, Eelke B. Lenselink, Julien Louvel, and Thea Mulder-Krieger
- Subjects
Pharmacology ,Structure-affinity relationships ,Pyrimidine ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Substituent ,Antagonist ,General Medicine ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Adenosine A1 receptor ,Adenosine A(1) receptor ,chemistry ,Docking (molecular) ,Drug Discovery ,Adenosine A(2A) receptor ,Antagonists ,Selectivity ,Diarylpyrimidines ,Biological evaluation - Abstract
We report the synthesis and biological evaluation of new 2-amino-4,5-diarylpyrimidines as selective antagonists at the adenosine A(1) receptor. The scaffold they are based upon is a deaza variation of a previously reported collection of 3-amino-5,6-diaryl-1,2,4-triazines, members of which had a sub-nanomolar affinity but limited selectivity over the A(2A) subtype. Initially, similar structure-affinity relationships at the 5-aryl ring were established, and then emphasis was put on increasing selectivity at the hA(1)AR by introducing substituents on the N-2-position, all the while maintaining a nanomolar affinity. Compound 3z, bearing a trans 4-hydroxycyclohexyl substituent, was identified as a potent (K-i(hA(1)AR) = 7.7 nM) and selective (K-i(hA(2)AAR) = 1389 nM) antagonist at the human adenosine A(1) receptor. Computational docking was effected at the A(1) and A(2A) subtypes, rationalizing the effect of the 4-hydroxycyclohexyl substituent on selectivity, in relation with the nature of the substituent on the 5-position of the pyrimidine. (C) 2016 Elsevier Masson SAS. All rights reserved.
- Published
- 2017
41. A covalent antagonist for the human adenosine A2A receptor
- Author
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Thomas J M Michiels, Laura H. Heitman, Xue Yang, Julien Louvel, Ad P. IJzerman, Eelke B. Lenselink, and Guo Dong
- Subjects
0301 basic medicine ,Adenosine ,Stereochemistry ,A2A adenosine receptor ,Covalent antagonist ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,0302 clinical medicine ,G protein-coupled receptors ,Radioligand binding ,medicine ,Receptor ,Molecular Biology ,G protein-coupled receptor ,chemistry.chemical_classification ,Chemistry ,Cell Biology ,A(2A) adenosine receptor ,Ligand (biochemistry) ,Adenosine receptor ,Amino acid ,030104 developmental biology ,Docking (molecular) ,Covalent bond ,030220 oncology & carcinogenesis ,medicine.drug - Abstract
The structure of the human A2A adenosine receptor has been elucidated by X-ray crystallography with a high affinity non-xanthine antagonist, ZM241385, bound to it. This template molecule served as a starting point for the incorporation of reactive moieties that cause the ligand to covalently bind to the receptor. In particular, we incorporated a fluorosulfonyl moiety onto ZM241385, which yielded LUF7445 (4-((3-((7-amino-2-(furan-2-yl)-[1, 2, 4]triazolo[1,5-a][1, 3, 5]triazin-5-yl)amino)propyl)carbamoyl)benzene sulfonyl fluoride). In a radioligand binding assay, LUF7445 acted as a potent antagonist, with an apparent affinity for the hA2A receptor in the nanomolar range. Its apparent affinity increased with longer incubation time, suggesting an increasing level of covalent binding over time. An in silico A2A-structure-based docking model was used to study the binding mode of LUF7445. This led us to perform site-directed mutagenesis of the A2A receptor to probe and validate the target lysine amino acid K153 for covalent binding. Meanwhile, a functional assay combined with wash-out experiments was set up to investigate the efficacy of covalent binding of LUF7445. All these experiments led us to conclude LUF7445 is a valuable molecular tool for further investigating covalent interactions at this receptor. It may also serve as a prototype for a therapeutic approach in which a covalent antagonist may be needed to counteract prolonged and persistent presence of the endogenous ligand adenosine.KEYWORDS: A2A adenosine receptor; Adenosine; Covalent antagonist; G protein-coupled receptors; Radioligand binding
- Published
- 2017
42. A yeast screening method to decipher the interaction between the adenosine A2B receptor and the C-terminus of different G protein α-subunits
- Author
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Eelke B. Lenselink, Rongfang Liu, Nick J. A. Groenewoud, Ad P. IJzerman, and Miriam C. Peeters
- Subjects
G protein-coupled receptor kinase ,GTPase-activating protein ,G protein ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Cell Biology ,Biology ,Receptor, Adenosine A2B ,GTP-Binding Protein alpha Subunits ,Protein Structure, Secondary ,Cellular and Molecular Neuroscience ,G beta-gamma complex ,Biochemistry ,Heterotrimeric G protein ,Humans ,Original Article ,5-HT5A receptor ,Amino Acid Sequence ,Molecular Biology ,Protein Binding ,G protein-coupled receptor ,G alpha subunit - Abstract
The expression of human G protein-coupled receptors (GPCRs) in Saccharomyces cerevisiae containing chimeric yeast/mammalian Gα subunits provides a useful tool for the study of GPCR activation. In this study, we used a one-GPCR-one-G protein yeast screening method in combination with molecular modeling and mutagenesis studies to decipher the interaction between GPCRs and the C-terminus of different α-subunits of G proteins. We chose the human adenosine A2B receptor (hA2BR) as a paradigm, a typical class A GPCR that shows promiscuous behavior in G protein coupling in this yeast system. The wild-type hA2BR and five mutant receptors were expressed in 8 yeast strains with different humanized G proteins, covering the four major classes: Gαi, Gαs, Gαq, and Gα12. Our experiments showed that a tyrosine residue (Y) at the C-terminus of the Gα subunit plays an important role in controlling the activation of GPCRs. Receptor residues R103(3.50) and I107(3.54) are vital too in G protein-coupling and the activation of the hA2BR, whereas L213(IL3) is more important in G protein inactivation. Substitution of S235(6.36) to alanine provided the most divergent G protein-coupling profile. Finally, L236(6.37) substitution decreased receptor activation in all G protein pathways, although to a different extent. In conclusion, our findings shed light on the selectivity of receptor/G protein coupling, which may help in further understanding GPCR signaling.
- Published
- 2014
43. Relative Binding Free Energy Calculations Applied to Protein Homology Models
- Author
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Thijs Beuming, Eelke B. Lenselink, Jun Qi, Woody Sherman, Michelle Lynn Hall, Daniel Cappel, and James E. Bradner
- Subjects
0301 basic medicine ,Binding free energy ,Protein Conformation ,General Chemical Engineering ,Degrees of freedom (statistics) ,Library and Information Sciences ,Molecular Dynamics Simulation ,Ligands ,01 natural sciences ,Article ,Free energy perturbation ,03 medical and health sciences ,Molecular dynamics ,Computational chemistry ,0103 physical sciences ,Animals ,Humans ,Statistical physics ,Representation (mathematics) ,Databases, Protein ,010304 chemical physics ,Chemistry ,Drug discovery ,Sampling (statistics) ,Proteins ,General Chemistry ,Computer Science Applications ,030104 developmental biology ,Structural Homology, Protein ,Drug Design ,Computer-Aided Design ,Thermodynamics ,Protein homology ,Protein Binding - Abstract
A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein–ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points—something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein–protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the “real” conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with full system flexibility and offers promise for the general application of FEP to homology models, although additional validation studies should be performed to further understand the limitations of the method and the scenarios where FEP will work best.
- Published
- 2016
44. Removal of Human Ether-à-go-go Related Gene (hERG) K+ Channel Affinity through Rigidity: A Case of Clofilium Analogues
- Author
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Elisabeth Klaasse, Johannes Brussee, João F. S. Carvalho, Eelke B. Lenselink, Julien Louvel, Marjolein Soethoudt, Adriaan P. IJzerman, and Zhiyi Yu
- Subjects
Patch-Clamp Techniques ,Stereochemistry ,hERG ,HUMAN ETHER-A-GO-GO-RELATED GENE ,Structure-Activity Relationship ,Drug Discovery ,Potassium Channel Blockers ,medicine ,Humans ,Molecule ,Cardiotoxicity ,biology ,Chemistry ,Drug discovery ,Clofilium ,Ether-A-Go-Go Potassium Channels ,Potassium channel ,Molecular Docking Simulation ,Quaternary Ammonium Compounds ,HEK293 Cells ,biology.protein ,Biophysics ,Molecular Medicine ,Anti-Arrhythmia Agents ,Linker ,medicine.drug - Abstract
Cardiotoxicity is a side effect that plagues modern drug design and is very often due to the off-target blockade of the human ether-à-go-go related gene (hERG) potassium channel. To better understand the structural determinants of this blockade, we designed and synthesized a series of 40 derivatives of clofilium, a class III antiarrhythmic agent. These were evaluated in radioligand binding and patch-clamp assays to establish structure-affinity relationships (SAR) for this potassium channel. Efforts were especially focused on studying the influence of the structural rigidity and the nature of the linkers composing the clofilium scaffold. It was shown that introducing triple bonds and oxygen atoms in the n-butyl linker of the molecule greatly reduced affinity without significantly modifying the pKa of the essential basic nitrogen. These findings could prove useful in the first stages of drug discovery as a systematic way of reducing the risk of hERG K(+) channel blockade-induced cardiotoxicity.
- Published
- 2013
45. Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening
- Author
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Gerard J. P. van Westen, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Willem Jespers, and Eelke B. Lenselink
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0301 basic medicine ,Virtual screening ,Ligand ,Protein Conformation ,General Chemical Engineering ,General Chemistry ,Computational biology ,Library and Information Sciences ,Biology ,Bioinformatics ,Crystallography, X-Ray ,Ligands ,Computer Science Applications ,Receptors, G-Protein-Coupled ,Molecular Docking Simulation ,03 medical and health sciences ,030104 developmental biology ,Docking (molecular) ,Drug Discovery ,Humans ,Interaction type ,Amino acid residue ,G protein-coupled receptor ,Protein Binding - Abstract
The expanding number of crystal structures of G protein-coupled receptors (GPCRs) has increased the knowledge on receptor function and their ability to recognize ligands. Although structure-based virtual screening has been quite successful on GPCRs, scores obtained by docking are typically not indicative for ligand affinity. Methods capturing interactions between protein and ligand in a more explicit manner, such as interaction fingerprints (IFPs), have been applied as an addition or alternative to docking. Originally IFPs captured the interactions of amino acid residues with ligands with specific definitions for the various interaction types. More complex IFPs now capture atom-atom interactions, such as in SYBYL, or fragment-fragment co-occurrences such as in SPLIF. Overall, most of the IFPs have been studied in comparison with docking in retrospective studies. For GPCRs it remains unclear which IFP should be used, if at all, and in what manner. Thus, the performance between five different IFPs was compared on five different representative GPCRs, including several extensions of the original implementations,. Results show that the more detailed IFPs, SYBYL and SPLIF, perform better than the other IFPs (Deng, Credo, and Elements). SPLIF was further tuned based on the number of poses, fingerprint similarity coefficient, and using an ensemble of structures. Enrichments were obtained that were significantly higher than initial enrichments and those obtained by 2D-similarity. With the increase in available crystal structures for GPCRs, and given that IFPs such as SPLIF enhance enrichment in virtual screens, it is anticipated that IFPs will be used in conjunction with docking, especially for GPCRs with a large binding pocket.
- Published
- 2016
46. A covalent antagonist for the human adenosine A
- Author
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Xue, Yang, Guo, Dong, Thomas J M, Michiels, Eelke B, Lenselink, Laura, Heitman, Julien, Louvel, and Ad P, IJzerman
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Adenosine ,Receptor, Adenosine A2A ,G protein-coupled receptors ,Radioligand binding ,Triazines ,A2A adenosine receptor ,Humans ,Original Article ,Triazoles ,Adenosine A2 Receptor Antagonists ,Covalent antagonist - Abstract
The structure of the human A2A adenosine receptor has been elucidated by X-ray crystallography with a high affinity non-xanthine antagonist, ZM241385, bound to it. This template molecule served as a starting point for the incorporation of reactive moieties that cause the ligand to covalently bind to the receptor. In particular, we incorporated a fluorosulfonyl moiety onto ZM241385, which yielded LUF7445 (4-((3-((7-amino-2-(furan-2-yl)-[1, 2, 4]triazolo[1,5-a][1, 3, 5]triazin-5-yl)amino)propyl)carbamoyl)benzene sulfonyl fluoride). In a radioligand binding assay, LUF7445 acted as a potent antagonist, with an apparent affinity for the hA2A receptor in the nanomolar range. Its apparent affinity increased with longer incubation time, suggesting an increasing level of covalent binding over time. An in silico A2A-structure-based docking model was used to study the binding mode of LUF7445. This led us to perform site-directed mutagenesis of the A2A receptor to probe and validate the target lysine amino acid K153 for covalent binding. Meanwhile, a functional assay combined with wash-out experiments was set up to investigate the efficacy of covalent binding of LUF7445. All these experiments led us to conclude LUF7445 is a valuable molecular tool for further investigating covalent interactions at this receptor. It may also serve as a prototype for a therapeutic approach in which a covalent antagonist may be needed to counteract prolonged and persistent presence of the endogenous ligand adenosine. Electronic supplementary material The online version of this article (doi:10.1007/s11302-016-9549-9) contains supplementary material, which is available to authorized users.
- Published
- 2016
47. Synthesis and evaluation of N-substituted 2-amino-4,5-diarylpyrimidines as selective adenosine A
- Author
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Georgios, Alachouzos, Eelke B, Lenselink, Thea, Mulder-Krieger, Henk, de Vries, Adriaan P, IJzerman, and Julien, Louvel
- Subjects
Structure-Activity Relationship ,Pyrimidines ,Molecular Structure ,Humans ,Computer Simulation ,Adenosine A1 Receptor Antagonists ,Protein Binding - Abstract
We report the synthesis and biological evaluation of new 2-amino-4,5-diarylpyrimidines as selective antagonists at the adenosine A
- Published
- 2016
48. Getting from A to B-exploring the activation motifs of the class B adhesion G protein-coupled receptor subfamily G member 4/GPR112
- Author
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Iris Mos, Thue W. Schwartz, Adriaan P. IJzerman, Eelke B. Lenselink, Martina Lucchesi, and Miriam C. Peeters
- Subjects
0301 basic medicine ,Subfamily ,Protein Conformation ,Protein domain ,Adenosine A2A receptor ,Biology ,Biochemistry ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,Protein structure ,Protein Domains ,Genetics ,Humans ,Amino Acid Sequence ,Receptor ,Molecular Biology ,Peptide sequence ,G protein-coupled receptor ,Cell biology ,030104 developmental biology ,HEK293 Cells ,Gene Expression Regulation ,Mutation ,Signal transduction ,Biotechnology ,Signal Transduction - Abstract
The adhesion G protein-coupled receptors [ADGRs/class B2 G protein-coupled receptors (GPCRs)] constitute an ancient family of GPCRs that have recently been demonstrated to play important roles in cellular and developmental processes. Here, we describe a first insight into the structure-function relationship of ADGRs using the family member ADGR subfamily G member 4 (ADGRG4)/GPR112 as a model receptor. In a bioinformatics approach, we compared conserved, functional elements of the well-characterized class A and class B1 secretin-like GPCRs with the ADGRs. We identified several potential equivalent motifs and subjected those to mutational analysis. The importance of the mutated residues was evaluated by examining their effect on the high constitutive activity of the N-terminally truncated ADGRG4/GPR112 in a 1-receptor-1-G protein Saccharomyces cerevisiae screening system and was further confirmed in a transfected mammalian human embryonic kidney 293 cell line. We evaluated the results in light of the crystal structures of the class A adenosine A2A receptor and the class B1 corticotropin-releasing factor receptor 1. ADGRG4 proved to have functionally important motifs resembling class A, class B, and combined elements, but also a unique highly conserved ADGR motif (H3.33). Given the high conservation of these motifs and residues across the adhesion GPCR family, it can be assumed that these are general elements of ADGR function.-Peeters, M. C., Mos, I., Lenselink, E. B., Lucchesi, M., IJzerman, A. P., Schwartz, T. W. Getting from A to B-exploring the activation motifs of the class B adhesion G protein-coupled receptor subfamily G member 4/GPR112.
- Published
- 2015
49. Scanning mutagenesis in a yeast system delineates the role of the NPxxY(x)(5,6)F motif and helix 8 of the adenosine A(2B) receptor in G protein coupling
- Author
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Adriaan P. IJzerman, Rongfang Liu, Eelke B. Lenselink, Dennis Nahon, and Beau le Roy
- Subjects
Models, Molecular ,G protein ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Biology ,Receptor, Adenosine A2B ,Biochemistry ,Protein Structure, Secondary ,Radioligand Assay ,GTP-Binding Proteins ,medicine ,Humans ,5-HT5A receptor ,Amino Acid Sequence ,Receptor ,G protein-coupled receptor ,Pharmacology ,Alanine ,Sulfonamides ,Computational Biology ,Adenosine receptor ,Molecular biology ,Adenosine ,Adenosine A2 Receptor Antagonists ,Xanthines ,Mutation ,Adenosine A2B receptor ,medicine.drug - Abstract
The adenosine receptor subfamily includes four subtypes: the A1, A2A, A2B and A3 receptors, which all belong to the superfamily of G protein-coupled receptors (GPCRs). The adenosine A2B receptor is the least investigated of the adenosine receptors, and the molecular mechanisms of its activation have hardly been explored. We used a single-GPCR-one-G protein yeast screening method in combination with mutagenesis studies, molecular modeling and bio-informatics to investigate the importance of the different amino acid residues of the NPxxY(x)6F motif and helix 8 in the human adenosine A2B receptor (hA2BR) activation. A scanning mutagenesis protocol was employed, yielding 11 single mutations and one double mutation of the NPxxY(x)6F motif and 16 single mutations of helix 8. The amino acid residues P287(7.50), Y290(7.53), R293(7.56) and I304(8.57) were found to be essential, since mutation of these amino acid residues to alanine led to a complete loss of function. Western blot analysis showed that mutant receptor R293(7.56)A was not expressed, whereas the other proteins were. Amino acid residues that are also important in receptor activation are: N286(7.49), V289(7.52), Y292(7.55), N294(8.47), F297(8.50), R298(8.51), H302(8.55) and R307(8.60). The mutation Y290(7.53)F lost 50% of efficacy, while F297(8.50)A behaved similar to wild type receptor. The double mutation, Y290(7.53)F/F297(8.50)Y, lost around 70% of efficacy and displayed a lower potency for the reference agonist 5'-(N-ethylcarboxamido)adenosine (NECA). This study provides new insight into the molecular interplay and impact of TM7 and helix 8 for hA2B receptor activation, which may be extrapolated to other adenosine receptors and possibly to other GPCRs.
- Published
- 2015
50. Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling
- Author
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Daniel S. Murrell, Thérèse E. Malliavin, Gerard J. P. van Westen, Andreas Bender, Eelke B. Lenselink, and Isidro Cortes-Ciriano
- Subjects
Computer science ,Cell ,0211 other engineering and technologies ,Context (language use) ,02 engineering and technology ,computer.software_genre ,Bayesian inference ,Biochemistry ,03 medical and health sciences ,symbols.namesake ,Structural Biology ,medicine ,Sensitivity (control systems) ,Representation (mathematics) ,Molecular Biology ,Gaussian process ,030304 developmental biology ,0303 health sciences ,Virtual screening ,021103 operations research ,Ligand ,Applied Mathematics ,Computer Science Applications ,medicine.anatomical_structure ,Meeting Abstract ,symbols ,Data mining ,DNA microarray ,Biological system ,computer ,Applicability domain - Abstract
Proteochemometrics (PCM) is a predictive bioactivity modelling method to simultaneously model the bioactivity of multiple ligands against multiple targets. Therefore, PCM permits to explore the selectivity and promiscuity of ligands on biomolecular systems of different complexity, such proteins or even cell-line models. In practice, each ligand-target interaction is encoded by the concatenation of ligand and target descriptors. These descriptors are then used to train a single machine learning model. This simultaneous inclusion of both chemical and target information enables the extra- and interpolation to predict the bioactivity of compounds on targets, which can be not present in the training set. In this thesis, a methodological advance in the field is firstly introduced, namely how Bayesian inference (Gaussian Processes) can be successfully applied in the context of PCM for (i) the prediction of compounds bioactivity along with the error estimation of the prediction; (ii) the determination of the applicability domain of a PCM model; and (iii) the inclusion of experimental uncertainty of the bioactivity measurements. Additionally, the influence of noise in bioactivity models is benchmarked across a panel of 12 machine learning algorithms, showing that the noise in the input data has a marked and different influence on the predictive power of the considered algorithms. Subsequently, two R packages are presented. The first one, Chemically Aware Model Builder (camb), constitues an open source platform for the generation of predictive bioactivity models. The functionalities of camb include : (i) normalized chemical structure representation, (ii) calculation of 905 one- and two-dimensional physicochemical descriptors, and of 14 fingerprints for small molecules, (iii) 8 types of amino acid descriptors, (iv) 13 whole protein sequence descriptors, and (iv) training, validation and visualization of predictive models. The second package, conformal, permits the calculation of confidence intervals for individual predictions in the case of regression, and P values for classification settings. The usefulness of PCM to concomitantly optimize compounds selectivity and potency is subsequently illustrated in the context of two application scenarios, which are: (a) modelling isoform-selective cyclooxygenase inhibition; and (b) large-scale cancer cell-line drug sensitivity prediction, where the predictive signal of several cell-line profiling data is benchmarked (among others): basal gene expression, gene copy-number variation, exome sequencing, and protein abundance data. Overall, the application of PCM in these two case scenarios let us conclude that PCM is a suitable technique to model the activity of ligands exhibiting uncorrelated bioactivity profiles across a panel of targets, which can range from protein binding sites (a), to cancer cell-lines (b).
- Published
- 2015
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