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Chris de Graaf

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Chris de Graaf; Gerdien E de Kloe; Paul J England; Albert J Kooistra; Martien Kuijer; Rob Leurs; Saskia Nijmeijer; Jacqueline van Muijlwijk-Koezen; Mark H P Verheij; Henry Vischer; Iwan J P De Esch
Small and colorful stones make beautiful mosaics: fragment-based chemogenomics.
Chimed Jansen; Hengming Ke; Albert J Kooistra; Kristina M Orrling; Thomas Seebeck; Hermann Tenor; Huanchen Wang; David Bailey; Iwan J P De Esch; Chris de Graaf; Rob Leurs
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure.
Albert J Kooistra; Rob Leurs; Luc Roumen; Iwan J P De Esch; Chris de Graaf
From heptahelical bundle to hits from the Haystack: structure-based virtual screening for GPCR ligands.

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All Publications

2013: Chris de Graaf; Gerdien E de Kloe; Paul J England; Albert J Kooistra; Martien Kuijer; Rob Leurs; Saskia Nijmeijer; Jacqueline van Muijlwijk-Koezen; Mark H P Verheij; Henry Vischer; Iwan J P De Esch
Small and colorful stones make beautiful mosaics: fragment-based chemogenomics.
Drug discovery today 2013;18(7-8):323-30.
2013: Chimed Jansen; Hengming Ke; Albert J Kooistra; Kristina M Orrling; Thomas Seebeck; Hermann Tenor; Huanchen Wang; David Bailey; Iwan J P De Esch; Chris de Graaf; Rob Leurs
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure.
Journal of medicinal chemistry 2013;56(5):2087-96.
2013: Albert J Kooistra; Rob Leurs; Luc Roumen; Iwan J P De Esch; Chris de Graaf
From heptahelical bundle to hits from the Haystack: structure-based virtual screening for GPCR ligands.
Methods in enzymology 2013;522():279-336.
2013: Sabine Schultes; Obbe P Zuiderveld; Iwan J P De Esch; Harald Engelhardt; Eric E J Haaksma; Rob Leurs; Luc Roumen; Chris de Graaf
Combining quantum mechanical ligand conformation analysis and protein modeling to elucidate GPCR-ligand binding modes.
ChemMedChem 2013;8(1):49-53.
2012: Maikel Wijtmans; Meritxell Canals; Hans Custers; Iwan J P De Esch; Chris de Graaf; Frans J J de Kanter; Marjolein Glas; Luc Roumen; Danny J Scholten; Martine J Smit; Marlies C A Vreeker; Rob Leurs
Chemical subtleties in small-molecule modulation of peptide receptor function: the case of CXCR3 biaryl-type ligands.
Journal of medicinal chemistry 2012;55(23):10572-83.
2012: Maikel Wijtmans; David Maussang; Azra Mujić-Delić; Danny J Scholten; Francesco Sirci; Martine J Smit; Meritxell Canals; Kristell L S Chatalic; Milagros Chong; Hans Custers; Iwan J P De Esch; Chris de Graaf; Elwin Janssen; Rob Leurs
Synthesis, modeling and functional activity of substituted styrene-amides as small-molecule CXCR7 agonists.
European journal of medicinal chemistry 2012;51():184-92.
2012: Saskia Nijmeijer; Chris de Graaf; Rob Leurs; Henry Vischer
Molecular pharmacology of histamine H4 receptors.
Frontiers in bioscience : a journal and virtual library 2012;17():2089-106.
2011: Chris de Graaf; Fabrizio Giordanetto; David Piwnica; Chantal Rein; Didier Rognan
Structure-based discovery of allosteric modulators of two related class B G-protein-coupled receptors.
ChemMedChem 2011;6(12):2159-69.
2011: Chris de Graaf; So Iwata; Vsevolod Katritch; Albert J Kooistra; Martien Kuijer; Tatsuro Shimamura; Mitsunori Shiroishi; Raymond C Stevens; Henry Vischer; Iwan J P De Esch; Rob Leurs
Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor.
Journal of medicinal chemistry 2011;54(23):8195-206.
2011: Enade P Istyastono; Albert J Kooistra; Rob Leurs; Herman D Lim; Saskia Nijmeijer; Luc Roumen; Andrea C van de Stolpe; Henry Vischer; Iwan J P De Esch; Chris de Graaf
Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies.
Journal of medicinal chemistry 2011;54(23):8136-47.
2011: Petra de Kruijf; Douglas S Auld; Chris de Graaf; Herman D Lim; Véronique A Renjaän; Luc Roumen; Martine J Smit; Maria L Webb; Jac C H M Wijkmans; Guido J R Zaman; Jiuqiao Zhao; Rob Leurs
Identification of a novel allosteric binding site in the CXCR2 chemokine receptor.
Molecular pharmacology 2011;80(6):1108-18.
2011: Atilla Akdemir; Daniel Bertrand; Sonia Bertrand; Chris de Graaf; Aldo Jongejan; Rob Leurs; Prakash Rucktooa; Titia K Sixma; August B Smit; Rene van Elk; Iwan J P De Esch
Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors.
Bioorganic & medicinal chemistry 2011;19(20):6107-19.
2011: Mark H P Verheij; Henry Vischer; Obbe P Zuiderveld; Chris de Graaf; Gerdien E de Kloe; Saskia Hulscher; Rob Leurs; Sarah C R Lummis; Saskia Nijmeijer; Linda Silvestri; Rogier A Smits; Andrew J Thompson; Jacqueline van Muijlwijk-Koezen; Iwan J P De Esch
Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H₄ and the ion channel serotonin 5-HT₃A.
Bioorganic & medicinal chemistry letters 2011;21(18):5460-4.
2011: Maikel Wijtmans; Chris de Graaf; Gerdien de Kloe; Enade P Istyastono; Judith Smit; Herman Lim; Ratchanok Boonnak; Saskia Nijmeijer; Rogier A Smits; Aldo Jongejan; Obbe Zuiderveld; Iwan J P De Esch; Rob Leurs
Triazole ligands reveal distinct molecular features that induce histamine H4 receptor affinity and subtly govern H4/H3 subtype selectivity.
Journal of medicinal chemistry 2011;54(6):1693-703.
2011: Enade P Istyastono; Chris de Graaf; Iwan J P De Esch; Rob Leurs
Molecular determinants of selective agonist and antagonist binding to the histamine H₄ receptor.
Current topics in medicinal chemistry 2011;11(6):661-79.
2010: Albert J Kooistra; Thomas W Binsl; Johannes H G M Van Beek; Chris de Graaf; Jaap Heringa
Electron density fingerprints (EDprints): virtual screening using assembled information of electron density.
Journal of chemical information and modeling 2010;50(10):1772-80.
2010: Herman D Lim; Chris de Graaf; Wen Jiang; Payman Sadek; Patricia M McGovern; Enade P Istyastono; Remko A Bakker; Iwan J P De Esch; Robin Thurmond; Rob Leurs
Molecular determinants of ligand binding to H4R species variants.
Molecular pharmacology 2010;77(5):734-43.
2009: Igor Shamovsky; Chris de Graaf; Lisa Alderin; Malena Bengtsson; Håkan Bladh; Lena Börjesson; Stephen Connolly; Hazel J Dyke; Marco van den Heuvel; Henrik Johansson; Bo-Göran Josefsson; Anna Kristoffersson; Tero Linnanen; Annea Lisius; Roope Männikkö; Bo Nordén; Steve Price; Lena Ripa; Didier Rognan; Alexander Rosendahl; Marco Skrinjar; Klaus Urbahns
Increasing selectivity of CC chemokine receptor 8 antagonists by engineering nondesolvation related interactions with the intended and off-target binding sites.
Journal of medicinal chemistry 2009;52(23):7706-23.
2009: Steven Ballet; Debby Feytens; Rien De Wachter; Magali De Vlaeminck; Ewa D Marczak; Severo Salvadori; Chris de Graaf; Didier Rognan; Lucia Negri; Roberta Lattanzi; Lawrence H Lazarus; Dirk Tourwé; Gianfranco Balboni
Conformationally constrained opioid ligands: the Dmt-Aba and Dmt-Aia versus Dmt-Tic scaffold.
Bioorganic & medicinal chemistry letters 2009;19(2):433-7.
2009: Chris de Graaf; Didier Rognan
Customizing G Protein-coupled receptor models for structure-based virtual screening.
Current pharmaceutical design 2009;15(35):4026-48.
2008: Chris de Graaf; Didier Rognan
Selective structure-based virtual screening for full and partial agonists of the beta2 adrenergic receptor.
Journal of medicinal chemistry 2008;51(16):4978-85.
2008: Chris de Graaf; Nicolas Foata; Ola Engkvist; Didier Rognan
Molecular modeling of the second extracellular loop of G-protein coupled receptors and its implication on structure-based virtual screening.
Proteins 2008;71(2):599-620.
2007: Chris de Graaf; Chris Oostenbrink; Peter H J Keizers; Barbara M A van Vugt-Lussenburg; Jan N M Commandeur; Nico P E Vermeulen
Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations.
European biophysics journal : EBJ 2007;36(6):589-99.
2007: Alois Bonifacio; André R Groenhof; Peter H J Keizers; Chris de Graaf; Jan N M Commandeur; Nico P E Vermeulen; Andreas W Ehlers; Koop Lammertsma; Cees Gooijer; Gert van der Zwan
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2007;12(5):645-54.
2007: Chris de Graaf; Chris Oostenbrink; Peter H J Keizers; Barbara M A van Vugt-Lussenburg; Robert A B van Waterschoot; Richard A Tschirret-Guth; Jan N M Commandeur; Nico P E Vermeulen
Molecular modeling-guided site-directed mutagenesis of cytochrome P450 2D6.
Current drug metabolism 2007;8(1):59-77.
2006: Peter H J Keizers; B R Van Dijk; Chris de Graaf; Barbara M A van Vugt-Lussenburg; Nico P E Vermeulen; Jan N M Commandeur
Metabolism of N-substituted 7-methoxy-4-(aminomethyl) -coumarins by cytochrome P450 2D6 mutants and the indication of additional substrate interaction points.
Xenobiotica; the fate of foreign compounds in biological systems 2006;36(9):763-71.
2006: Chris de Graaf; Chris Oostenbrink; Peter H J Keizers; Tushar van der Wijst; Aldo Jongejan; Nico P E Vermeulen
Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking.
Journal of medicinal chemistry 2006;49(8):2417-30.
2006: Robert A B van Waterschoot; Peter H J Keizers; Chris de Graaf; Nico P E Vermeulen; Richard A Tschirret-Guth
Topological role of cytochrome P450 2D6 active site residues.
Archives of biochemistry and biophysics 2006;447(1):53-8.
2006: Aike Stortelder; Peter H J Keizers; Chris Oostenbrink; Chris de Graaf; Petra De Kruijf; Nico P E Vermeulen; Cees Gooijer; Jan N M Commandeur; Gert van der Zwan
Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy.
The Biochemical journal 2006;393(Pt 3):635-43.
2005: Peter H J Keizers; Loek H M Schraven; Chris de Graaf; Mats Hidestrand; Magnus Ingelman-Sundberg; Ben R van Dijk; Nico P E Vermeulen; Jan N M Commandeur
Role of the conserved threonine 309 in mechanism of oxidation by cytochrome P450 2D6.
Biochemical and biophysical research communications 2005;338(2):1065-74.
2005: Barbara M A Lussenburg; Peter H J Keizers; Chris de Graaf; Mats Hidestrand; Magnus Ingelman-Sundberg; Nico P E Vermeulen; Jan N M Commandeur
The role of phenylalanine 483 in cytochrome P450 2D6 is strongly substrate dependent.
Biochemical pharmacology 2005;70(8):1253-61.
2005: Peter H J Keizers; Chris de Graaf; Frans J J de Kanter; Chris Oostenbrink; K Anton Feenstra; Jan N M Commandeur; Nico P E Vermeulen
Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation.
Journal of medicinal chemistry 2005;48(19):6117-27.
2005: Chris de Graaf; Nico P E Vermeulen; K Anton Feenstra
Cytochrome p450 in silico: an integrative modeling approach.
Journal of medicinal chemistry 2005;48(8):2725-55.
2005: Chris de Graaf; Pavel Pospisil; Wouter Pos; Gerd Folkers; Nico P E Vermeulen
Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.
Journal of medicinal chemistry 2005;48(7):2308-18.
2005: Aldo Jongejan; Chris de Graaf; Nico P E Vermeulen; Rob Leurs; Iwan J P De Esch
The role and application of in silico docking in chemical genomics research.
Methods in molecular biology (Clifton, N.J.) 2005;310():63-91.
2004: Peter H J Keizers; Barbara M A Lussenburg; Chris de Graaf; Letty M Mentink; Nico P E Vermeulen; Jan N M Commandeur
Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: crucial role in 7-methoxy-4-(aminomethyl)-coumarin metabolism.
Biochemical pharmacology 2004;68(11):2263-71.
2004: René van Herwijnen; Chris de Graaf; Harrie A J Govers; John R Parsons
Estimation of kinetic parameter for the biotransformation of three-ring azaarenes by the phenanthrene-degrading strain Sphingomonas sp. LH128.
Environmental toxicology and chemistry / SETAC 2004;23(2):331-8.