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2010

Comparison of murine and human estrogen sulfotransferase inhibition in vitro and in silico-implications for differences in activity, subunit dimerization and substrate inhibition

Stjernschantz, E. M., Reinen, J., Meinl, W., George, B. J., Glatt, H., Vermeulen, N. P. E. & Oostenbrink, C., 2010, In : Molecular and Cellular Endocrinology. 137, 1-2, p. 127-140

Research output: Contribution to JournalArticleAcademicpeer-review

Dimerization
Computer Simulation
Substrates
Enzymes
estrone sulfotransferase

Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

Vasanthanathan, P., Olsen, L., Jørgensen, F. S., Vermeulen, N. P. E. & Oostenbrink, C., Aug 2010, In : Drug Metabolism and Disposition. 38, 8, p. 1347-1354 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Cytochrome P-450 CYP1A2
Ligands
Cytochrome P-450 Enzyme System
Mechanics
Static Electricity

Cytochrome P450 BM3 Mutants as NOVEL Biocatalytic TOOLS for Regioselective Hydroxylation of Steroids

Rea, V., Kolkman, J. A., Vottero, E., Honing, M., Wijmenga, S., Vermeulen, N. P. E. & Commandeur, J. N. M., Aug 2010, In : Drug Metabolism Reviews. 42, p. 285-286

Research output: Contribution to JournalArticleProfessional

Determination and identification of estrogenic compounds generated with biosynthetic enzymes using hyphenated screening assays, high resolution mass spectrometry and off-line NMR

de Vlieger, J. S. B., Kolkman, A. J., Ampt, K. A. M., Commandeur, J. N. M., Vermeulen, N. P. E., Kool, J., Wijmenga, S. S., Niessen, W. M. A., Irth, H. & Honing, M., 2010, In : Journal of Chromatography B. 878, 7-8, p. 667-674 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Liquid chromatography
Liquid Chromatography
Mass spectrometry
Assays
Mass Spectrometry

Endocrine disrupting chemicals-linking internal exposure to vitellogenin levels and ovotestis in Abramis brama from Dutch surface waters

Reinen, J., Suter, M. J. F., Vogeli, A. C., Fernandez, M. F., Kiviranta, H., Eggen, R. I. L. & Vermeulen, N. P. E., 2010, In : Environmental Toxicology and Pharmacology. 30, p. 209-223

Research output: Contribution to JournalArticleAcademicpeer-review

Vitellogenins
Endocrine Disruptors
Surface waters
Fish
Fishes

Functional characterization of eight human cytochrome P450 1A2 gene variants by recombinant protein expression

Brito Palma, B., Silva e Sousa, M., Vosmeer, C. R., Lastdrager, J., Rueff, J., Vermeulen, N. P. E. & Kranendonk, M., 2010, In : Pharmacogenomics Journal. p. 1-11 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Cytochrome P-450 CYP1A2
Recombinant Proteins
Apoproteins
Genes
Carcinogens

Metabolism related toxicity of diclofenac in yeast as model system

van Leeuwen, J. S., Vredenburg, G., Dragovic, S., Tjong, T. F., Vos, J. C. & Vermeulen, N. P. E., 2010, In : Toxicology Letters. nov 24, p. 200(3): 162-8 doi: 10.1016/j.toxlet.2010.11.010.

Research output: Contribution to JournalArticleAcademicpeer-review

Diclofenac
Metabolism
Yeast
Toxicity
Yeasts

Role of human glutathione S-transferases in the inactivation of reactive metabolites of clozapine.

Dragovic, S., Boerma, J. S., van Bergen, L., Vermeulen, N. P. E. & Commandeur, J. N. M., 2010, In : Chemical Research in Toxicology. 23, 9, p. 1467-1476

Research output: Contribution to JournalArticleAcademicpeer-review

Clozapine
Metabolites
Glutathione Transferase
Pharmaceutical Preparations
Detoxification

Role of Human Glutathione S-Transferases on the Inactivation of Reactive Drug METABOLITES of Clozapine

Dragovic, S., Boerma, J. S., van Bergen, L., Vermeulen, N. P. E. & Commandeur, J. N. M., Aug 2010, In : Drug Metabolism Reviews. 42, p. 67-67

Research output: Contribution to JournalArticleProfessional

Subunits Rip1 and Cox9p of the respiratory chain contribute to diclofenac-induced mitochondrial dysfunction

van Leeuwen, J. S., Orij, R., Luttik, M. A., Smits, G. J., Vermeulen, N. P. E. & Vos, J. C., 2010, In : Microbiology. dec 9

Research output: Contribution to JournalArticleAcademicpeer-review

Diclofenac
Electron Transport
Reactive Oxygen Species
Respiration
Electron Transport Complex III

The role of biotransformation in the estrogenicity of xenobiotics

Reinen, J., 2010

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

The role of water molecules in computational Drug Design

de Beer, S., Vermeulen, N. P. E. & Oostenbrink, B. C., 2010, In : Current Topics in Microbiology and Immunology. 10, p. 55-66

Research output: Contribution to JournalArticleAcademicpeer-review

2011

Active site substitution A82W improves regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalised by spin relaxation NMR studies

Rea, V., Kolkman, ER., Vottero, E. R., Stronks, E. J., Ampt, K. A., Honing, M., Vermeulen, N. P. E., Wijmenga, S. S. & Commandeur, J. N. M., 2011, (Accepted/In press) In : The Biochemist.

Research output: Contribution to JournalArticleAcademicpeer-review

Application of CYP102A1M11H as a tool for the generation of protein adducts of reactive drug metabolites

Boerma, J. S., Vermeulen, N. P. E. & Commandeur, J. N. M., 2011, In : Chemical Research in Toxicology. 24, 8, p. 1263-1274 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Metabolites
troglitazone
Glutathione S-Transferase pi
Cysteine
Clozapine

Application of cytochrome P450 BM3 mutants as biocatalysts for the profiling of estrogen receptor binding metabolites of the mycotoxin zearalenone

Reinen, J., Kalma, L., Begheijn, S., Heus, F. A. H., Commandeur, J. N. M. & Vermeulen, N. P. E., 2011, In : Xenobiotica. 41, 1, p. 59-70 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Zearalenone
Mycotoxins
Metabolites
Estrogen Receptors
Cytochrome P-450 Enzyme System

Conventional and novel approaches in generating and characterization of reactive intermediates from drugs/drug candidates

Orhan, H. & Vermeulen, N. P. E., May 2011, In : Current Drug Metabolism. 12, 4, p. 383-394 12 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Metabolites
Pharmaceutical Preparations
Biotransformation
Toxicity
Molecules

Diclofenac inhibits tumor necrosis factor-a-induced nuclear factor-kB activation causing synergic hepatocyte apoptosis

Frederiksson, L., Herpers, B., Benedetti, G., Matadin, Q., Puigvert, J. C., de Bont, H., Dragovic, S., Vermeulen, N. P. E., Commandeur, J. N. M., Danen, E., de Graauw, M. & van de Water, B., 2011, In : Hepatology. 53, 6, p. 383-394 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Diclofenac
Hepatocytes
Tumor Necrosis Factor-alpha
Apoptosis
Hep G2 Cells

Efficient screening of cytochrome P450 BM3 mutants for their metabolic activity and diversity toward a wide set of drug-like molecules in chemical space

Reinen, J., van Leeuwen, J. S., Li, Y., Sun, L., Grootenhuis, P. D. J., Decker, C. J., Saunders, J., Vermeulen, N. P. E. & Commandeur, J. N. M., 2011, (Accepted/In press) In : Drug Metabolism and Disposition.

Research output: Contribution to JournalArticleAcademicpeer-review

Cytochrome P-450 Enzyme System
Pharmaceutical Preparations
Liquid Chromatography
Libraries
Mass Spectrometry

Identification of CYP1A2 ligands by structure-based and ligand-based virtual screening

Vasanthanathan, P., Lastdrager, J., Oostenbrink, C., Commandeur, J. N. M., Vermeulen, N. P. E., Jorgensen, F. S. & Olsen, L., Sep 2011, In : MedChemComm. 2, 9, p. 853-859

Research output: Contribution to JournalArticleAcademicpeer-review

drug resistance
Saccharomyces
Diclofenac
homeostasis
protein kinase C

Managing the challenge of chemically reactive metabolites in drug development

Park, B. K., Boobis, A., Clarke, S., Goldring, C. E. P., Jones, D. T., Kenna, J. G., Lambert, C., Laverty, H. G., Naisbitt, D. J., Nelson, S., Nicoll-Griffith, D. A., Obach, R. S., Routledge, P., Smith, D. A., Tweedie, D. J., Vermeulen, N., Williams, D. P., Wilson, I. D. & Baillie, T. A., Apr 2011, In : Nature Reviews Drug Discovery. 10, 4, p. 292-306 15 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Drug Industry
Pharmaceutical Preparations
Pharmaceutical Chemistry
Risk Management
Drug Discovery

Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase

de Beer, S. B. A., Glättli, A., Hutzler, J., Vermeulen, N. P. E. & Oostenbrink, B. C., 2011, In : Journal of Computational Chemistry.

Research output: Contribution to JournalArticleAcademicpeer-review

Role of residue 87 in substrate selectivity and regioselectivity of drug-metabolizing cytochrome P450 CYP102A1 M11

Vottero, E. R., Rea, V., Lastdrager, J., Honing, M., Vermeulen, N. P. E. & Commandeur, J. N. M., 2011, In : Journal of Biological Inorganic Chemistry - JBIC. 16, 6, p. 899-912 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Regioselectivity
Cytochrome P-450 Enzyme System
Drug Residues
Substrates
Enzymes

Role of residue 87 in the activity and regioselectivity of clozapine metabolism by drug-metabolizing CYP102A1 M11H: application for structural characterization of clozapine GSH conjugates

Rea, V., Dragovic, S., Boerma, J. S., de Kanter, F. J. J., Vermeulen, N. P. E. & Commandeur, J. N. M., 2011, (Accepted/In press) In : Drug Metabolism and Disposition. p. 39(12): 2411-20. doi: 10.1124/dmd.111.041046.

Research output: Contribution to JournalArticleAcademicpeer-review

Clozapine
Pharmaceutical Preparations
Amino Acids
Glutathione Transferase
Drug-Related Side Effects and Adverse Reactions

The estrogen receptor, environmental estrogens and the role of cytochrome P450 in bioactivation

van Lipzig, M. M. H., 2011

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Yeast as a model eukaryote in drug safety studies: New insights on diclofenac-induced toxicity

van Leeuwen, J. S., 2011

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File
2012

Active Site Substitution A82W Improves the Regioselectivity of Steroid Hydroxylation by Cytochrome P450 BM3 Mutants As Rationalized by Spin Relaxation Nuclear Magnetic Resonance Studies

Rea, V., Kolkman, A. J., Vottero, E. R., Stronks, E. J., Ampt, K. A., Honing, M., Vermeulen, N. P. E., Wijmenga, S. S. & Commandeur, J. N. M., 2012, In : Biochemistry. 51, 3, p. 750-760

Research output: Contribution to JournalArticleAcademicpeer-review

Regioselectivity
Hydroxylation
Cytochrome P-450 Enzyme System
Catalytic Domain
Substitution reactions

Application of free energy calculations for drug design

de Beer, S. B. A., 2012

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

A single active site mutation inverts stereoselectivity of 16-hydroxylation of testosterone catalyzed by engineered cytochrome P450 BM3.

Venkataraman, H., de Beer, SB., Bergen, LA., van Essen, N., Geerke, D. P., Vermeulen, N. P. E. & Commandeur, J. N. M., 2012, In : ChemBioChem. 13, 4, p. 520-523

Research output: Contribution to JournalArticleAcademicpeer-review

Cytochrome P450 BM3 as versatile biocatalytic tool in drug development

Rea, V., 2012

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Differential involvement of mitochondrial dysfunction, cytochrome P450 activity, and active transport in the toxicity of structurally related NSAIDs

van Leeuwen, J. S., Unlü, B., Vermeulen, N. P. E. & Vos, J. C., 2012, In : Toxicology in Vitro. 26, 2, p. 197-205

Research output: Contribution to JournalArticleAcademicpeer-review

Active Biological Transport
Cytochrome P-450 Enzyme System
Toxicity
Anti-Inflammatory Agents
Pharmaceutical Preparations

Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants

De Beer, S. B., Venkataraman, H., Geerke, D. P., Oostenbrink, C. & Vermeulen, N. P. E., 2012, In : Journal of Chemical Information and Modeling. 52, 8, p. 2139-2148

Research output: Contribution to JournalArticleAcademicpeer-review

Norisoprenoids
Hydroxylation
Cytochrome P-450 Enzyme System
Free energy
energy

Interactions of organophosphates with keratins in the cornified epithelium of human skin

Verstappen, D. R. W., Hulst, A. G., Fidder, A., Vermeulen, N. P. E. & Noort, D., 2012, In : Chemico-Biological Interactions. 197, 2-3, p. 93-102

Research output: Contribution to JournalArticleAcademicpeer-review

Organophosphates
Keratins
Skin
Epithelium
Tyrosine

Malleability and versatility of Cytochrome P450 active sites studied by molecular simulations

Oostenbrink, B. C., de Ruiter, A., Hritz, J. & Vermeulen, N. P. E., 2012, In : Current Drug Metabolism. 13, 2, p. 190-196

Research output: Contribution to JournalArticleAcademicpeer-review

Glutathione S-Transferase pi
Diclofenac
Glutathione Transferase
Proteins
Peptides

Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants

Venkataraman, H., de Beer, S. B. A., Geerke, D. P., Vermeulen, N. P. E. & Commandeur, J. N. M., 2012, In : Advanced Synthesis and Catalysis. 354, 11-12, p. 2172-2184

Research output: Contribution to JournalArticleAcademicpeer-review

Norisoprenoids
Hydroxylation
Enantiomers
Cytochrome P-450 Enzyme System
Stereoselectivity

The role of protein plasticity in computational rationalization studies on regioselectivity in testosterone hydroxylation by Cytochrome P450 BM3 mutants

de Beer, S. B. A., van Bergen, L. A. H., Keijzer, K., Rea, V., Venkataraman, H., Fonseca Guerra, C., Bickelhaupt, F. M., Vermeulen, N. P. E., Commandeur, J. N. M. & Geerke, D. P., 2012, In : Current Drug Metabolism. 13, 2, p. 155-166

Research output: Contribution to JournalArticleAcademicpeer-review

Regioselectivity
Hydroxylation
Cytochrome P-450 Enzyme System
Plasticity
Testosterone

Yeast as a humanized model organism for biotransformation-related toxicity

van Leeuwen, J. S., Vermeulen, N. P. E. & Vos, J. C., 2012, In : Current Drug Metabolism. 13, 10, p. 1464-1475

Research output: Contribution to JournalArticleAcademicpeer-review

Biotransformation
Yeast
Toxicity
Yeasts
Enzymes
2013

Characterisation of Human Cytochrome P450s Involved in the Bioactivation of Clozapine

Dragovic, S., Gunness, P., Ingelman-Sundberg, M., Vermeulen, N. P. E. & Commandeur, J. N. M., 2013, In : Drug Metabolism and Disposition. 41, 3, p. 651-658

Research output: Contribution to JournalArticleAcademicpeer-review

Clozapine
Cytochromes
Cytochrome P-450 CYP3A
Cytochrome P-450 CYP2D6
Liver
p38 Mitogen-Activated Protein Kinases
Biotransformation
Screening
Phosphotransferases
Small Molecule Libraries

Effect of human glutathione S-transferases on glutathione-dependent inactivation of cytochrome P450-dependent reactive intermediates of diclofenac.

Dragovic, S., Boerma, J. S., Vermeulen, N. P. E. & Commandeur, J. N. M., 2013, In : Chemical Research in Toxicology. 26, 11, p. 1632-1641

Research output: Contribution to JournalArticleAcademicpeer-review

Diclofenac
Glutathione Transferase
Cytochrome P-450 Enzyme System
Glutathione
Liver

Glutathione-S-transferases: tools and targets for characterization of chemically reactive drug metabolites

Boerma, J. S., 2013

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Reconstitution of the interplay between cytochrome P450 and human glutathione S-transferases in clozapine metabolism in yeast.

Vredenburg, G., Vassell, K. P., Commandeur, J. N. M., Vermeulen, N. P. E. & Vos, J. C., 2013, In : Toxicology Letters. 222, 3, p. 247-256

Research output: Contribution to JournalArticleAcademicpeer-review

Clozapine
Glutathione Transferase
Metabolism
Yeast
Cytochrome P-450 Enzyme System

Role of genetic polymorphisms of drug metabolising enzymes in idiosyncratic drug reactions In vitro to in vivo translation

Dragovic, S., 2013

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Translational strategies for identifying chemically reactive metabolites as cause for Adverse Drug Reactions

Vermeulen, N. P. E., 28 Aug 2013, In : Toxicology Letters. 221, p. S28-S28

Research output: Contribution to JournalArticleProfessional

Urinary lipid and protein oxidation products upon halothane, isoflurane, or sevoflurane anesthesia in humans: potential biomarkers for a subclinical nephrotoxicity

Orhan, H., Sahin, A., Sahin, G., Aypar, U. & Vermeulen, N. P. E., 2013, In : Biomarkers. 18, 1, p. 73-81

Research output: Contribution to JournalArticleAcademicpeer-review

Isoflurane
Biomarkers
Halothane
Anesthesia
Lipids
2014

Application of engineered cytochrome P450 mutants as biocatalysts for the synthesis of benzylic and aromatic metabolites of fenamic acid NSAIDs

Venkataraman, H., Verkade-Vreeker, M. C. A., Capoferri, L., Geerke, D. P., Vermeulen, N. P. E. & Commandeur, J. N. M., 15 Oct 2014, In : Bioorganic and Medicinal Chemistry. 22, 20, p. 5613-5620

Research output: Contribution to JournalArticleAcademicpeer-review

Cytochrome P450-mediated bioactivation of mefenamic acid to quinoneimine intermediates and inactivation by human glutathione S-transferases

Venkataraman, H., Den Braver, M. W., Vermeulen, N. P. E. & Commandeur, J. N. M., 15 Dec 2014, In : Chemical Research in Toxicology. 27, 12, p. 2071-2081 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Mefenamic Acid
Glutathione Transferase
Cytochrome P-450 Enzyme System
Hydroxy Acids
Metabolites

Effect of human glutathione S-transferase hGSTP1-1 polymorphism on the detoxification of reactive metabolites of clozapine, diclofenac and acetaminophen

Dragovic, S., Venkataraman, H., Begheijn, S., Vermeulen, N. P. E. & Commandeur, J. N. M., 2014, In : Toxicology Letters. 224, 2, p. 272-281

Research output: Contribution to JournalArticleAcademicpeer-review

Detoxification
Diclofenac
Clozapine
Acetaminophen
Metabolites

Engineered cytochrome P450 BM3 mutants as biocatalysts for metabolite production: Applications in biotechnology and toxicology

Venkataraman, H., 2014

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File