Research Output 1977 2018

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2017
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.

Research output: Scientific - peer-reviewArticle

Open Access

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: Scientific - peer-reviewArticle

2016

Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity.

Reinen, J. R., Postma, G., Tump, C., Bloemberg, T., Engel, J., Vermeulen, N. P. E., Commandeur, J. N. M. & Honing, M. 2016 In : Analytical and Bioanalytical Chemistry. 408, p. 1425-1443

Research output: Scientific - peer-reviewArticle

Open Access

Evidence-based selection of training compounds for use in the mechanism-based integrated prediction of drug-induced liver injury in man.

Dragovic, S., Vermeulen, N. P. E., Gerets, H. H., Hewitt, P. G., Ingelman-Sundberg, M., Park, B. K., Juhila, S., Snoeys, J. & Weaver, R. J. 2016 In : Archives of Toxicology. 90, 12, p. 2979-3003

Research output: Scientific - peer-reviewArticle

Open Access
Open Access

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations.

Capoferri, L., Leth, R., ter Haar, E., Mohanty, A. K., Grootenhuis, P. D. J., Vottero, E. R., Commandeur, J. N. M., Vermeulen, N. P. E., Jorgensen, F. S., Olsen, L. & Geerke, D. P. 2016 In : Proteins. 84, 3, p. 383-396

Research output: Scientific - peer-reviewArticle

Response to 'The path forward on endocrine disruptors requires focus"

Autrup, H., Barile, F., 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. E. 2016 In : Toxicological Sciences. 149, 2, p. 273-274

Research output: Scientific - peer-reviewArticle

Response to “The Path Forward on Endocrine Disruptors Requires Focus”

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. Feb 2016 In : Toxicological sciences : an official journal of the Society of Toxicology. 149, 2, p. 273-4 2 p.

Research output: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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

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

Research output: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle

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: Scientific - peer-reviewArticle