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  • Nico P.E. Vermeulen
2019

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation

Rifai, E. A., van Dijk, M., Vermeulen, N. P. E., Yanuar, A. & Geerke, D. P., 11 Sep 2019, In : Journal of Chemical Information and Modeling. 59, 9, p. 4018-4033 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Open Access
2018

Acetaminophen reduces the protein levels of high affinity amino acid permeases and causes tryptophan depletion

Huseinovic, A., Dekker, S. J., Boogaard, B., Vermeulen, N. P. E., Kooter, J. M. & Vos, J. C., Oct 2018, In : Amino Acids. 50, 10, p. 1377-1390 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants

Luirink, R. A., Dekker, S. J., Capoferri, L., Kuiper, C. L., Janssen, L. F. H., Ari, M. E., Vermeulen, N. P. E., Vos, J. C., Commandeur, J. N. M. & Geerke, D. P., Jul 2018, In : Journal of Inorganic Biochemistry. 184, p. 115-122 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine

Huseinovic, A., van Dijk, M., Vermeulen, N. P. E., van Leeuwen, F., Kooter, J. M. & Vos, J. C., Mar 2018, In : Toxicology in Vitro. 47, p. 259-268 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Effect of UGT2B7*2 and CYP2C8*4 polymorphisms on diclofenac metabolism

Lazarska, K. E., Dekker, S. J., Vermeulen, N. P. E. & Commandeur, J. N. M., 1 Mar 2018, In : Toxicology Letters. 284, 1 March, p. 70-78 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Glutathione S-transferase P1 protects against Amodiaquine Quinoneimines-induced cytotoxicity but does not prevent activation of endoplasmic reticulum stress in HepG2 cells

Zhang, Y., den Braver-Sewradj, S. P., den Braver, M. W., Hiemstra, S., Vermeulen, N. P. E., van de Water, B., Commandeur, J. N. M. & Vos, J. C., 18 Apr 2018, In : Frontiers in Pharmacology. 9, APRIL, p. 1-13 13 p., 388.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Inter-individual variability in activity of the major drug metabolizing enzymes in liver homogenates of 20 Individuals

den Braver-Sewradj, S. P., den Braver, M. W., van Dijk, M., Zhang, Y., Dekker, S. J., Wijaya, L., Vermeulen, N. P. E., Richert, L., Commandeur, J. N. M. & Vos, J. C., 2018, In : Current Drug Metabolism. 19, 4, p. 370-381 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Linking cytochrome P450 enzymes from Mycobacterium tuberculosis to their cognate ferredoxin partners

Ortega Ugalde, S., de Koning, C. P., Wallraven, K., Bruyneel, B., Vermeulen, N. P. E., Grossmann, T. N., Bitter, W., Commandeur, J. N. M. & Vos, J. C., Nov 2018, In : Applied Microbiology and Biotechnology. 102, 21, p. 9231-9242 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Reduction and Scavenging of Chemically Reactive Drug Metabolites by NAD(P)H: Quinone Oxidoreductase 1 and NRH:Quinone Oxidoreductase 2 and Variability in Hepatic Concentrations

den Braver-Sewradj, S. P., den Braver, M. W., Toorneman, R. M., Van Leeuwen, S., Zhang, Y., Dekker, S. J., Vermeulen, N. P. E., Commandeur, J. N. M. & Vos, J. C., 19 Feb 2018, In : Chemical Research in Toxicology. 31, 2, p. 116-126 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2017
Open Access

Characterization of human cytochrome P450 mediated bioactivation of amodiaquine and its major metabolite N-desethylamodiaquine

Zhang, Y., Vermeulen, N. P. E. & Commandeur, J. N. M., 1 Mar 2017, In : British Journal of Clinical Pharmacology. 83, 3, p. 572-583 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors

van Dijk, M., Ter Laak, A. M., Wichard, J. D., Capoferri, L., Vermeulen, N. P. E. & Geerke, D. P., 25 Sep 2017, In : Journal of Chemical Information and Modeling. 57, 9, p. 2294-2308 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Direct comparison of UDP-glucuronosyltransferase and cytochrome P450 activities in human liver microsomes, plated and suspended primary human hepatocytes from five liver donors

den Braver-Sewradj, S. P., den Braver, M. W., Baze, A., Decorde, J., Fonsi, M., Bachellier, P., Vermeulen, N. P. E., Commandeur, J. N. M., Richert, L. & Vos, J. C., 1 Aug 2017, In : European Journal of Pharmaceutical Sciences. 109, p. 96-110 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

Capoferri, C. L., van Dijk, M., Rustenburg, A. S., Wassenaar, T., Kooi, D. P., Rifai, E. A., Vermeulen, N. P. E. & Geerke, D. P., 2017, In : Journal of Cheminformatics. 9, 58, p. 1-13 13 p., 58.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Generic method for the absolute quantification of glutathione S-conjugates: Application to the conjugates of acetaminophen, clozapine and diclofenac

den Braver, M. W., Vermeulen, N. P. E. & Commandeur, J. N. M., 1 Mar 2017, In : Journal of Chromatography B. 1046, p. 185-194 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Legacy data sharing to improve drug safety assessment: the eTOX project

Sanz, F., Pognan, F., Steger-Hartmann, T., Díaz, C., Cases, M., Pastor, M., Marc, P., Wichard, J., Briggs, K., Watson, D. K., Kleinöder, T., Yang, C., Amberg, A., Beaumont, M., Brookes, A. J., Brunak, S., Cronin, M. T. D., Ecker, G. F., Escher, S., Greene, N. & 17 others, Guzmán, A., Hersey, A., Jacques, P., Lammens, L., Mestres, J., Muster, W., Northeved, H., Pinches, M., Saiz, J., Sajot, N., Valencia, A., van der Lei, J., Vermeulen, N. P. E., Vock, E., Wolber, G., Zamora, I. & eTOX, Dec 2017, In : Nature Reviews Drug Discovery. 16, 12, p. 811-812 2 p.

Research output: Contribution to JournalArticleAcademicpeer-review

The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae

Huseinovic, A., van Leeuwen, J., van Welsem, T., Stulemeijer, I., van Leeuwen, F., Vermeulen, N. P. E., Kooter, J. M. & Vos, J. C., 14 Mar 2017, In : PLoS ONE. 12, 3, p. 1-19 19 p., e0173573.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2015

Activation of the anticancer drugs cyclophosphamide and ifosfamide by cytochrome P450 BM3 mutants

Vredenburg, G., den Braver-Sewradj, S., van Vugt-Lussenburg, B. M. A., Vermeulen, N. P. E., Commandeur, J. N. M. & Vos, J. C., 5 Jan 2015, In : Toxicology Letters. 232, 1, p. 182-92 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Application of a Continuous-Flow Bioassay to Investigate the Organic Solvent Tolerability of Cytochrome P450 BM3 Mutants

Reinen, J., van Hemert, D., Vermeulen, N. P. E. & Commandeur, J. N. M., Dec 2015, In : Journal of Biomolecular Screening. 20, 10, p. 1246-55 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biosynthesis of a steroid metabolite by an engineered Rhodococcus erythropolis strain expressing a mutant cytochrome P450 BM3 enzyme

Venkataraman, H., te Poele, E. M., Rosłoniec, K. Z., Vermeulen, N., Commandeur, J. N. M., van der Geize, R. & Dijkhuizen, L., 18 Jun 2015, In : Applied Microbiology and Biotechnology. 99, 11, p. 4713-4721 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Characterization of human cytochrome P450s involved in the bioactivation of tri-Ortho-Cresyl phosphate (ToCP)

Reinen, J., Nematollahi, L., Fidder, A., Vermeulen, N. P. E., Noort, D. & Commandeur, J. N. M., 20 Apr 2015, In : Chemical Research in Toxicology. 28, 4, p. 711-721 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project

Sanz, F., Carrio, P., Lopez, O., Capoferri, L., Kooi, D. P., Vermeulen, N. P. E., Geerke, D. P., Montanari, F., Ecker, G. F., Schwab, C. H., Kleinoeder, T., Magdziarz, T. & Pastor, M., Jun 2015, In : Molecular Informatics. 34, 6-7, p. 477-484

Research output: Contribution to JournalArticleAcademicpeer-review

Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation

Capoferri, L., Verkade-Vreeker, M. C. A., Buitenhuis, D., Commandeur, J. N. M., Pastor, M., Vermeulen, N. P. E. & Geerke, D. P., 9 Nov 2015, In : PLoS ONE. 10, 11

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Mass spectrometric identification of isocyanate-induced modifications of keratins in human skin

Hulst, A. G., Verstappen, D. R. W., Van Der Riet - Van Oeveren, D., Vermeulen, N. P. E. & Noort, D., 22 Jun 2015, In : Chemico-Biological Interactions. 237, p. 141-150 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Mini-dialysis tubes as tools to prepare drug-protein adducts of P450-dependent reactive drug metabolites

Boerma, J. S., Elias, N. S., Vermeulen, N. P. E. & Commandeur, J. N. M., 25 Jan 2015, In : Journal of Pharmaceutical and Biomedical Analysis. 103, p. 17-25

Research output: Contribution to JournalArticleAcademicpeer-review

Principles of pharmacology and toxicology also govern effects of chemicals on the endocrine system

Autrup, H., Barile, F. A., Blaauboer, B. J., Degen, G. H., Dekant, W., Dietrich, D., Domingo, J. L., Gori, G. B., Greim, H., Hengstler, J. G., Kacew, S., Marquardt, H., Pelkonen, O., Savolainen, K. & Vermeulen, N. P., 1 Jul 2015, In : Toxicological Sciences. 146, 1, p. 11-15 5 p., kfv082.

Research output: Contribution to JournalArticleAcademicpeer-review

Selective whole-cell biosynthesis of the designer drug metabolites 15- or 16-betahydroxynorethisterone by engineered Cytochrome P450 BM3 mutants

Reinen, J., Vredenburg, G., Klaering, K., Vermeulen, N. P. E., Commandeur, J. N. M., Honing, M. & Vos, J. C., 1 Nov 2015, In : Journal of Molecular Catalysis B. Enzymatic. 121, p. 64-74 11 p., 3212.

Research output: Contribution to JournalArticleAcademicpeer-review

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

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

Human NAD(P)H:quinone oxidoreductase 1 (NQO1)-mediated inactivation of reactive quinoneimine metabolites of diclofenac and mefenamic acid

Vredenburg, G., Elias, N. S., Venkataraman, H., Hendriks, D. F. G., Vermeulen, N. P. E., Commandeur, J. N. M. & Vos, J. C., 21 Apr 2014, In : Chemical Research in Toxicology. 27, 4, p. 576-86 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Towards automated binding affinity prediction using an iterative linear interaction energy approach

Vosmeer, C. R., Pool, R., van Stee, M. F., Peric-Hassler, L., Vermeulen, N. P. E. & Geerke, D. P., 2014, In : International Journal of Molecular Sciences. 15, 1, p. 798-816 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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

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

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

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

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

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

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

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

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

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