Total 23 results found.
Tag: Biotransformation, Bioactivation Biocatalysis Ordering

Position: PhD student

Room:  P2.54Tel: +31 20 59 87522Email: h.venkataraman@vu.nl

Vanina Rea, PhD

Position: PhD student

Room: P2.40 Tel: +31 20 5987593 Email: vrea@few.vu.nl

Sanja Dragovic MSc.

Position: PhD student

Room: P2.40 Tel: +31 20 5987593Email: sdragov@few.vu.nl

Jan-Simon Boerma, PhD

Position: PhD student

Room: P2.40Tel: +31 20 59 87593Email: j.s.boerma@vu.nl

Position: Post-doc

Room: Tel:Email: 

 

 

Dr. Jelle Reinen

Position: Post-doc

In December 2004, Jelle Reinen started his PhD research within the Division of Molecular Toxicology at the Vrije Universiteit, under supervision of Prof. Dr. N.P.E. Vermeulen, where he studied the role of biotransformation in the estrogenicity of xenobiotics. Besides studying the effects of endocrine disrupting chemicals (EDCs), both during his PhD project and later on as a postdoctoral fellow (since 2009), Jelle has been involved in the evaluation of the applicability of novel mutants of bacterial cytochrome P450 BM3 for large scale production of drug metabolites. This project was performed in close collaboration with Vertex Pharmaceuticals and from January 2009 until June 2009 part of this research project has been performed at the department of Drug Innovation at Vertex Pharmaceuticals (San Diego, CA, USA). Currently, his research focuses on the efficient screening of P450 BM3 mutant libraries for their metabolic activity and diversity towards drug-like molecules and the efficient application of P450 BM3 mutants as biocatalysts for large scale production of drug metabolites.

Room: P2.75BTel: +31 20 5987593Email: reinen@few.vu.nl

 

Dr. Kevin Augustijn

Position: Post-doc

Kevin Augustijn obtained his PhD at the adenovirus replication group of Prof. Dr. Peter van der Vliet, UMC, Utrecht, where he studied the interaction of human transcription factors using a combination of biochemical assays and structural biology (NMR spectroscopy at the group of Prof. Dr. Rob Kaptein, Utrecht University). After this, he joined the malaria research group of Dr. Chris Janse, Dept. of Parasitology, LUMC, where he studied parasite-host interactions in the rodent malaria parasite Plasmodium berghei. In 2009, he switched to the Molecular Toxicology group of Prof. Dr. Nico Vermeulen, VU Amsterdam, where he started as project manager supervising a TI Pharma project on biomarkers for adverse drug reactions. Later (2010) he was involved in a pan-European education and training programme for IMI-JU called SafeSciMET. This project organizes 20 course modules on drug safety sciences in a collaborative effort of academia and pharmaceutical industry. In 2012, he started on a second IMI JU project: MIP-DILI. This project aims to develop new assays for predicting drug-induced liver injury. Having been active in a number of different fields in molecular biology (transcription, structural biology, parasitology, immunology), he is a good all-round scientist with a "helicopter view" approach to problems. As project manager, he handles reporting, financial management, dissemination, compound databases and biological sample collection.

 

Room: P2.46Tel: +31 20 59 87600Email: k.d.augustijn@vu.nl 

Dr. Chris Vos

Position: Assistant Professor

Dr. ir. J.C. Vos studied Molecular Sciences at the Agricultural University of Wageningen. He received his PhD in 1993 at the University of Amsterdam for his work carried out at the European Molecular Biology Laboratory (EMBL) at Heidelberg, Germany, on vaccinia virus gene regulation. He spend two post-doctoral terms at the Dutch Cancer Institute in Amsterdam studying (i) DNA transposition in Caenorhabditis elegans (ii) the structure of the human Transporter Associated with Antigen Processing. In 2000, he moved to the section of Biochemistry and Molecular Biology (BMB) of the Vrije Universiteit focusing on the macromolecular interactions involved in the biogenesis of ribosomes in Saccharomyces cerevisiae. Since june 2006, he is member of the section of Molecular Toxicology, studying stress-response in yeast related to drug bioactivation by Cyt P450 biotransformation.

Room: KA 283aTel: +31 20 5987569Email: jc.vos@few.vu.nl

 

 

Dr. Chris Oostenbrink

Position: Assistant Professor

Chris Oostenbrink studied both Chemistry and Pharmacochemistry at the Vrije Universiteit, Amsterdam. He graduated twice in 2000 with specialisations in Theoretical Chemistry and Computational Medicinal Chemistry, in both cases cum laude. In 2004 he obtained his PhD at the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland, in the group of prof. W.F. van Gunsteren on the calculation of (binding) free energies in biomolecular simulations. In October 2004, he was appointed Assistent professor Computational Medicinal Chemistry and Toxicology (CMCT) at the VU. In 2005 he received two ‘young talent’ grants, a Bioinformatics Breakthrough grant from NWO-Horizon, and a VENI-grant from NWO-CW. In his work he is aiming to inter-connect computational and experimental approaches to study biomolecular systems and to show that computational tools studying protein structure and dynamics and protein-ligand interactions are complementary to experiments. Since 2009, Chris Oostenbrink has been appointed group leader in Molecular Modeling and Simulation at BOKU University, Vienna, and part-time as assistant-professor within the Division of Molecular and Computational Toxicology. See also his personal website.

Room: P2.62Tel: +31 20 5987606Email: c.oostenbrink@few.vu.nlWebsite: www.few.vu.nl/~oostnbrk

Dr. Jacqueline van Muijlwijk-Koezen

Position: Assistant Professor

Dr. Jacqueline van Muijlwijk-Koezen studied both Chemistry and Pharmacochemistry at VU University Amsterdam and graduated in 1994. She also combined both studies in her PhD research at VU University on molecular modeling and synthesis of new antagonists for the human adenosine A3 receptor. Part of the work she performed at Leiden University. In 2000, she started teaching mathematics at a high school, in combination with a study in education and didactics. She became a chemistry and physics teacher in 2002 at the Archimedes teacher education of Utrecht University.

Van Muijlwijk-Koezen returned to the Department of Chemistry and Pharmaceutical Sciences in 2003 as an assistant professor, with focus on education in life sciences. In 2006, she was appointed project manager, being responsible for the pre-bachelor education in all beta-disciplines and strengthening the connection between secondary schools and VU University. She initiated the development of post-graduate courses for teachers. She joined the Medicinal Chemistry research group in 2008. Her main interests are development and organization of education combined with a research focus on drug design and synthesis

Room: P2.64Tel: +31 20 5987611Email: je.van.muijlwijk@few.vu.nl

Dr. Daan Geerke

Position: Assistant Professor

In 2007, Daan Geerke obtained his PhD degree within the Laboratory for Physical Chemistry at the ETH Zürich, under supervision of Prof. Dr. Wilfred F. van Gunsteren. Afterwards he joined the research group of Dr. Julia E. Rice and Dr. William C. Swope at the IBM Almaden Research Center in San Jose, California, for a postdoctoral fellowship. In 2009 Daan Geerke has been appointed Assistant-Professor within the MCT research group of Prof. Dr. Nico P.E. Vermeulen at VU University. Currently, he is supervising a senior scientist and three PhD students, and he lectures a variety of bachelor and master courses in the fields of computational chemistry, (bio-)molecular modeling, structural biology and (statistical) thermodynamics. His research focuses on in silico rationalization and prediction of drug metabolism and action upon binding to flexible enzymes such as human and bacterial Cytochrome P450s, proteases or methyl transferases, in direct collaboration with ‘wet-chemistry’ colleagues within MCT,/VU, medical centers and industry. In addition he has since many years worked on development of biomolecular force fields and on inclusion of quantum and electronic polarization effects in simulation. He has published more than 40 scientific publications within these research fields. In 2009, he has been awarded a NWO-Veni grant, in 2013, he has been awarded a NWO-Vidi grant, in 2015 a NWO / NLeSC eScience grant (together with prof. Gunnar Klau / CWI) and since 2016 several HPC grants from the VU High Performance Computing council. In addition, he has been coordinator of the scientific activities at VU University in the context of the IMI-JU eTOX project on in silico prediction of toxicities.

Room: O|2 03E11Tel: +31 20 59 87606Email: d.p.geerke@vu.nl

Dr. Jan Commandeur

Position: Associate Professor

Dr. Commandeur studied Pharmacochemistry at the VU University Amsterdam. He graduated in 1985 with a specialization in Molecular Toxicology. He obtained his PhD. in 1991. Dr. Commandeur's interest lies in the investigation of the role of drug metabolizing enzymes, notably human cytochrome P450s, in the bioactivation of drugs, characterization of the reactive drug metabolites and their cellular targets,  and the identification of enzymes involved in detoxification of reactive intermediates (glutathione S-transferase and NQO1). In addition he is interested in the development of novel P450s which can be used as biocatalysts for large scale production of human drug metabolies and which can serve as model proteins for biochemical and biophysical studies into the mechanism of action of P450s. Amongst others, he is coordinator of the masterprogram Drug Discovery and Safety, track Drug Disposition and Safety Assessment (DDS-DDSA) and organizer of the Post-doctoral Course on Molecular Toxicology (yearly), the SafeSciMet-course “Biochemical and Molecular Toxicology” (bi-annually) and the ULLA Drug Metabolism course (bi-annually). He is member of the editorial board of Toxicology Letters and referee of many toxicological journals.

Room: P2.56

Tel: +31 20 5987595Email: jnm.commandeur@few.vu.nl

 

Prof. dr. Peter Grootenhuis

Position: Professor 'virtual screening and design'

In June 2005, Dr Peter Grootenhuis was appointed in Amsterdam as ‘extra-ordinary’ professor at a part-time chair, entitled: ‘ADME, Virtual Screening and Design’. Grootenhuis graduated in Chemistry at the University of Utrecht and received in 1987 his PhD-degree from Prof. D. Reinhoudt, University of Twente. After that he did a 2 years post-doc with Prof. Kollman at the University of California at San Francisco. He was subsequently employed by Organon, Combichem, Dupont, Bristol-Meyers Squibb and Deltagen. Grootenhuis is currently Senior Director ‘Discovery Chemistry’ at Vertex Pharmaceuticals in San Diego, USA. He has published over 100 scientific papers and is co-inventor of 20 patents. Amongst others, he received the Gold Medal of the Royal Dutch Chemical Society. In Amsterdam, Grootenhuis will be teaching computational drug discovery and collaborate in research on pre-experimental (i.e. virtual) ADME screening and modeling, with emphasis on Cytochromes P450.

Email: P.Grootenhuis@few.vu.nl  Peter_Grootenhuis@sd.vrtx.com

Prof.dr. Nico Vermeulen

Position: Head of Division of Molecular Toxicology

Professor Vermeulen graduated in Chemistry in 1975 at the Catholic University of Nijmegen. In 1980 he obtained his PhD in Pharmacology from the University of Leiden. In 1985 he was appointed professor of Molecular Toxicology at the Vrije Universiteit, Amsterdam.

Amongst others he is organizer of the yearly (Dutch) Post-academic Course on General Toxicology, the yearly international LACDR/EUFEPS course on High-Throughput Drug Metabolism and Disposition and of the PharmSciFair 2005 in Nice, a member of the Committee for the Registration of Toxicologists, chairman of the Section Pharmacochemistry of the Royal Netherlands Chemical Society (KNCV), a member of the Future Strategies Committee of the KNCV and councillor of the European Society of Biochemical Pharmacology (ESBP). In 2012 he chaired the first Joint MDO/European ISSX Meeting in Noordwijk, The Netherlands.

He was/is President-elect (2000-2001), President (2002-2003), Past-president (2004-2005) and Honorary Life-time member of the International Society for the Study of Xenobiotics (ISSX). In 2006, he received the European ISSX Scientific Achievement Award, and in 2011 an Honorary Doctorate from the University of Copenhagen.

Professor Vermeulen is on the editorial boards of the journals Biomarkers, Biomedical & Environmental Sciences, Biochemical Pharmacology, Chemico-Biological Interactions, Chirality, Chemistry & Biodiversity, Chemical Research in Toxicology, Drug Metabolism Reviews, Expert Opinions in Drug Metabolism & Toxicology, Toxicology and Xenobiotica. He is associate editor of Current Drug Metabolism/Drug Metabolism Letters and editor of Environmental Toxicology & Pharmacology.

Work of him and his group is since 2001 taken up in the ISI-list of Highly Cited Researchers.

 

Room: P2.22Tel: +31 20 5987590Email: n.p.e.vermeulen@vu.nl

CV [pdf]

The Biotransformation, Bioactivation & Biocatalysis research group

 

People involved: Staff: Jan N.M. Commandeur, Nico P.E. VermeulenPostdocs: Jelle ReinenPhD Students: Sanja Dragovic, Michiel den Braver, Shalenie Sewradj, Marlies Verkade-Vreeker, Stefan Dekker, Yongjie Zhang, Daan Verstappen, Katarzyna Lazarska

 

Research activities:The aim of the research of the Biotransformation, Bioactivation & Biocatalysis group is to elucidate the molecular mechanisms underlying as yet poorly understood adverse drug reactions (ADR). Is is well-established that drug metabolism and factors interfering with drug metabolism (drug-drug interaction, genetic polymorphism) play an important role in most ADR. In a number of cases, drug toxicity is the result from the formation of highly reactive drug metabolites, which may react to biomacromolecules and thereby interfere with their biological functions. Also, drug metabolites might have potent pharmacologically activity, which may contribute to the drug action, but which may also cause undesired pharmacological side-effects.

Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations Bren U, Oostenbrink BC J. Chem. Inf. Model., 2012, 52, 1573-1582 DOI:10.1021/ci300118x

Prof. dr. Nico Vermeulen from the Division of Molecular Toxicology and his staff members Dr. Jan Commandeur and Dr. Chris Vos have obtained a large grant for an Innovative Medicine Initiative project. With this funding, they aim to develop new test systems for drugs causing drug-induced liver injury in humans.

The Innovative Medicine Initiative project is entitled 'Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury'. It will address the improvement of existing and the development of novel in vivo and in vitro test systems for the prediction of drug-induced liver injury in humans. Drug-induced liver injury is main leading cause of liver failure and transplantation in western countries.

The total budget of the Innovative Medicine Initiative project is 34M EUR. Of this amount, 1.5M EUR is covering a 5-year contribution to the Division of Molecular Toxicology. With this grant, the division can hire 3 PhD students and a post-doc researcher and support them with significant additional funds for bench fees and equipment. This research project is the third Innovative Medicine Initiative project of group of Nico Vermeulen. In 2010, the IMI-SafeSciMET and IMI-eTOX projects were started.

Non-clinical test cascade

The consortium working on 'Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury' comprises key opinion leaders from universities, the biotechnology sector and the pharmaceutical industry. They share a common goal of improving the limited predictability or current drug-induced liver injury test systems.

The ultimate purpose is to develop a novel, non-clinical test cascade for this disease. This test cascade will be mechanism-based and/or of physiological, pharmacological and pathological relevance to drug-induced liver injury. The goal is to utilize the test cascade within the pharmaceutical industry to enable selection of drug candidates that have reduced propensity to cause drug-induced liver injury in humans.

Click here for more details on this project.

Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants Harini Venkataraman, Stephanie B. A. de Beer, Daan P. Geerke, Nico P. E. Vermeulen, Jan N. M. Commandeur Advanced Synthesis & Catalysis, Volume 354, Issue 11-12, pages 2172–2184, August 13, 2012

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants; Stephanie B.A. de Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P.E. Vermeulen; J. Chem. Inf. Model., 2012, 52 (8), pp 2139–2148; DOI: 10.1021/ci300243n

Combination of biotransformation by P450 BM3 mutants with on-line post-column bioaffinity and mass spectrometric profiling as a novel strategy to diversify and characterize p38α kinase inhibitors; Vanina Rea , David Falck , Jeroen Kool , Frans J. J. de Kanter , Jan N. M. Commandeur , Nico P. E. Vermeulen , Wilfried M. A. Niessen and Maarten Honing ; Med. Chem. Commun., 2013,4, 371-377 DOI: 10.1039/C2MD20283B

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