Nico Vermeulen

em. prof. dr.

  • De Boelelaan 1108, O|2 Lab Building (3E-09)

    1081 HZ Amsterdam

1977 …2019
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Research Output 1977 2019

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. p. 4018-4033 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Sirtuin 1
Molecular mechanics
mechanic
Free energy
Ligands

Applicability and performance of linear interaction energy based binding affinity calculation

Rifai, E. A., 2019, 183 p.

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

Open Access
File
Open Access
Sulfaphenazole
Floxacillin
Cytochrome P-450 CYP3A
Cytochromes
Hydroxylation

Mistaken identity: Paracetamol induces amino acid starvation through mimicry of tyrosine and changes ubiquitin homeostasis

Huseinovic, A., 2019, 202 p.

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

Open Access
File
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
Amino Acid Transport Systems
Acetaminophen
Tryptophan
Proteins
Yeast

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

Floxacillin
Hydroxylation
Cytochrome P-450 Enzyme System
Metabolites
Enzymes
Open Access
File

Drug induced liver injury: assessment of inter-individual variation in the balance of bioactivation and inactivation as risk factor

den Braver, M. W., 2018, 288 p.

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

Open Access
File

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
Acetaminophen
Drug-Related Side Effects and Adverse Reactions
Yeast
Toxicity
Saccharomyces cerevisiae

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
Diclofenac
Polymorphism
Metabolism
Liver
Chemical and Drug Induced Liver Injury

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
Endoplasmic Reticulum Stress
Hep G2 Cells
Amodiaquine
Glutathione Transferase
Glutathione
High performance liquid chromatography
Glutathione Transferase
Liver
Sulfates
Assays

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., 8 Jan 2018, In : Current Drug Metabolism. 19, 4, p. 370-381 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Liver
Glucuronosyltransferase
Oxidoreductases
Cytochromes
Glutathione Transferase

Inter-individual variation in hepatic drug metabolism: The potential of in vitro assays in unraveling the role of metabolism in drug induced liver toxicity

den Braver-Sewradj, S. P., 2018, 252 p.

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

Open Access
File

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
Ferredoxins
Mycobacterium tuberculosis
Cytochrome P-450 Enzyme System
Oxidation-Reduction
Genome

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
Scavenging
Metabolites
NAD
Oxidoreductases
Liver
2017
Open Access
Free energy
free energy
Ligands
Drug Design
Molecular Dynamics Simulation

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

Amodiaquine
Cytochrome P-450 Enzyme System
Liver Microsomes
Cytochromes
Cytochrome P-450 CYP3A

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
Aromatase Inhibitors
Cytochrome P-450 Enzyme System
energy
interaction
workflow

Development of human Cytochrome P450 competent genotoxicity tester bacterial systems for high throughput screening: Functional characterization of human Cytochrome P450 1A2 polymorphic variants

Espadinha de Brito Palma, B. J., 2017, 233 p.

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

Open Access
File

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

Glucuronosyltransferase
Liver Microsomes
Human Activities
Cytochrome P-450 Enzyme System
Hepatocytes

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: Contribution to JournalArticleAcademicpeer-review

Open Access
Pipelines
Ligands
Free energy
energy
ligands

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

o-Phthalaldehyde
Diclofenac
Clozapine
Acetylcysteine
Acetaminophen
Amodiaquine
Glutathione Transferase
Liver
NAD
Toxicity

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 othersGuzmán, 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

Information Dissemination
Safety
Pharmaceutical Preparations

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
acetaminophen
Acetaminophen
ubiquitin
Ubiquitin
Yeast
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, 5, p. 1425-1443 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Characterization of cytochrome P450 isoforms involved in sequential two-step bioactivation of diclofenac to reactive p-benzoquinone imines.

den Braver, M. W., Sewradj, S. P., Vermeulen, N. P. E. & Commandeur, J. N. M., 2016, In : Toxicology Letters. 253, p. 46-54

Research output: Contribution to JournalArticleAcademicpeer-review

Different reactive metabolites of nevirapine require distinct glutathione S-transferase isoforms for bio-inactivation

Dekker, S. J., Vos, J., Vermeulen, N. P. & Commandeur, J. N., 16 Sep 2016, In : Toxicology Letters. 29, 12, p. 2136-2144 9 p.

Research output: Contribution to JournalArticleProfessional

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: Contribution to JournalArticleAcademicpeer-review

Open Access

Improving the iterative linear interaction energy approach using automated recognition of configurational transitions.

Vosmeer, C. R., Kooi, D. P., Capoferri, L., Terpstra, M. M., Vermeulen, N. P. E. & Geerke, D. P., 2016, In : Journal of Molecular Modeling. 1, 31.

Research output: Contribution to JournalArticleAcademicpeer-review

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: Contribution to JournalArticleAcademicpeer-review

Inter-donor variability of phase I/phase II metabolism of three reference drugs in cryopreserved primary human hepatocytes in suspension and monolayer.

Sewradj, S. P., den Braver, M. W., Vermeulen, N. P. E., Commandeur, J. N. M., Richert, L. & Vos, J. C., 2016, In : Toxicology in Vitro. 33, p. 71-79 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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. 149, 2, p. 273-274 2 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Simulation of interindividual differences in inactivation of reactive para-benzoquinone imine metabolites of diclofenac by glutathione S-transferases in human liver cytosol.

den Braver, M. W., Zhang, Y., Venkataraman, H., Vermeulen, N. P. E. & Commandeur, J. N. M., 2016, In : Toxicology Letters. 255, p. 52-62

Research output: Contribution to JournalArticleAcademicpeer-review

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

Ifosfamide
Cyclophosphamide
Cytochrome P-450 Enzyme System
Chemical activation
Pharmaceutical Preparations

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

Bioassay
Mixed Function Oxygenases
Biological Assay
Organic solvents
Cytochrome P-450 Enzyme System

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

Rhodococcus
Cytochrome P-450 Enzyme System
Steroids
Enzymes
17-Ketosteroids

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

Cytochromes
Phosphates
Butyrylcholinesterase
Metabolites
Liver

Improved description of complex plasticity and interactions in protein-ligand simulations

Vosmeer, C. R., 2015, 175 p.

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

Open Access
File
proteins
ligands

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

Interplay between phase I and phase II biotransformation of drugs: In vitro approaches to study the formation and fate of reactive metabolites

Vredenburg, G., 2015, 173 p.

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

Open Access
File
Biotransformation
Pharmaceutical Preparations
In Vitro Techniques

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

Isocyanates
Keratins
Skin
Lysine
Bony Callus

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

Endocrine System
Toxicology
Pharmacology
Endocrine Disruptors
Health risks