Molecular and Computational Toxicology

Division of Molecular and Computational Toxicology

.\ MolTox ..\ Dept. Chemistry and Pharmaceutical Sciences ...\\ Faculty of Science

Members of the division as of November 2020 - Covid times. Location, Netherlands (Amsterdam, Hoofddorp, Leiden) and India - via Zoom. [Other group photos]

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The Division of Molecular and Computational Toxicology is specialised in developing computational and human in vitro (non-animal) based strategies for the understanding of the molecular mechanisms of chemical-induced toxicity in order to better predict chemical safety in humans.

The research combines and integrates three main tracks:
(1) Phase I and phase II metabolism and transport (phase III), including the influences of polymorphisms;
(2) Molecular mechanisms of chemical- and nanomaterial- induced cellular perturbations (primarily kidney and liver cells);
(3) Computational methods for site of metabolism prediction including molecular docking and dynamics..

The laboratory is specialised in analytical chemistry, cell culture, toxicity determination, omic analysis, molecular docking and dynamics. In vitro models include human primary cells, human cell lines and induced human Pluripotent Stem Cell derived cells.

Address:
Division of Molecular and Computational Toxicology,
Department of Chemistry and Pharmaceutical Sciences,
Amsterdam Institute for Molecules, Medicines and Systems,
Vrije Universiteit Amsterdam, De Boelelaan, 1108,
1081 HZ Amsterdam,
The Netherlands.
Floor 3, O|2 building.
[ Google map link ]
email p.jennings@vu.nl, e.v.langemeijer@vu.nl

Team

Senior Scientific Staff

PhD Students

Prof. Dr. Paul Jennings (chair)
Dr. Jan Commandeur
Dr. Daan Geerke
Dr. Chris Vos
Dr. Anja Wilmes
Dr. Ellen Langemeijer

Former:
Prof. dr. Nico Vermeulen
Dr. Marc van Dijk

Technicial Staff

Daniel Da Costa Pereira
Elisabeth Naderlinger

Koen Visscher
Kasia Lazarska
Rosa Luirink
Giada Carta
Cormac Murphy
Vidya Chandrasekaran
Liliana Capinha
Tamara Meijer

Recently completed:

Dr. Sandra Ortega Ugalde A new target for an old enemy
Dr. Eko Rifai Applicability and performance of linear interaction energy based binding affinity calculation
Dr. Angelina Huseinovic -istaken Identity.
Dr. Stefan Dekker Characterization of biotransformation enzymes involved in Adverse Drug Reactions.
Dr. Michiel W. den Braver Drug induced liver injury
Dr. Shalenie P. den Braver-Sewradj Inter-individual variation in hepatic drug metabolism
Dr. Yongjie Zhang In vitro and cellular systems for the characterization of bioactivating and inactivating drug metabolizing enzymes in adverse drug reactions

Open Position(s)

Assistant professor in xenobiotic metabolism and analytical toxicology: Application has closed.

Publications

All Publications [ Link ]

Recent publications

2020: Multiparametric assessment of mitochondrial respiratory inhibition in HepG2 and RPTEC/TERT1 cells using a panel of mitochondrial targeting agrochemicals. W. van der Stel, G. Carta, J. Eakins, S. Darici, J. Delp, A. Forsby, S. H. Bennekou, I. Gardner, M. Leist, E. H. J. Danen, P. Walker, B. van de Water, and P. Jennings. Journal https://www.ncbi.nlm.nih.gov/pubmed/32607615 10.1007/s00204-020-02792-5

2020: New approach methodologies (NAMs) for human-relevant biokinetics predictions: Meeting the paradigm shift in toxicology towards an animal-free chemical risk assessment. A. Punt, H. Bouwmeester, B. J. Blaauboer, S. Coecke, B. Hakkert, D. F. G. Hendriks, P. Jennings, N. I. Kramer, S. Neuhoff, R. Masereeuw, A. Paini, Aacm Peijnenburg, M. Rooseboom, M. L. Shuler, I. Sorrell, B. Spee, M. Strikwold, A. D. Van der Meer, M. Van der Zande, M. Vinken, H. Yang, P. M. J. Bos, and M. B. Heringa. Journal https://www.ncbi.nlm.nih.gov/pubmed/32521035 10.14573/altex.2003242

2020: Acetylene containing cyclo(L-Tyr-L-Tyr)-analogs as mechanism-based inhibitors of CYP121A1 from Mycobacterium tuberculosis. S. Ortega Ugalde, K. Wallraven, A. Speer, W. Bitter, T. N. Grossmann, and J. N. M. Commandeur. Journal 177, 113938 https://www.ncbi.nlm.nih.gov/pubmed/32224137 10.1016/j.bcp.2020.113938

2020: Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation. E. A. Rifai, V. Ferrario, J. Pleiss, and D. P. Geerke. Journal 16, 1300-1310 https://www.ncbi.nlm.nih.gov/pubmed/31894691 10.1021/acs.jctc.9b00890

2020: Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment. C. Rivetti, T. E. H. Allen, J. B. Brown, E. Butler, P. L. Carmichael, J. K. Colbourne, M. Dent, F. Falciani, L. Gunnarsson, S. Gutsell, J. A. Harrill, G. Hodges, P. Jennings, R. Judson, A. Kienzler, L. Margiotta-Casaluci, I. Muller, S. F. Owen, C. Rendal, P. J. Russell, S. Scott, F. Sewell, I. Shah, I. Sorrel, M. R. Viant, C. Westmoreland, A. White, and B. Campos. Journal 62, 104692 https://www.ncbi.nlm.nih.gov/pubmed/31669395 10.1016/j.tiv.2019.104692

2020: Polarisable force fields: what do they add in biomolecular simulations? V. S. Inakollu, D. P. Geerke, C. N. Rowley, and H. Yu. Journal 61, 182-190 https://www.ncbi.nlm.nih.gov/pubmed/32044671 10.1016/j.sbi.2019.12.012

Highlights

	MolTox Bachelor Students, Summer Langereis and Floor Slooter recieve the runner up prize at the Pharmaceutical Sciences Bachelor Project ceremony, presented by Prof. Prof. Dr. Célia Fonseca Guerra. O2 building, January 2020.
	Congratulations to Eko Rifai who received the Shukri Award for the best oral presentation at the AFPS-ICAPPS conference 2019 in Bali, Indonesia, in October 2019. https://afps2019.id The award was given by Management & Science University (MSU), Malaysia (https://www.msu.edu.my). In the picture, Prof. Dr. Eddy Yusuf and Eko Rifai. 🦆Link to tweet: https://twitter.com/PauloJennings/status/1192822724919484418
Congratulations to Sandra and Vidya for their AIMMS talk and AIMMS poster prize at the AIMMS day 18th April, 2019. https://www.aimms.vu.nl/en 🦆 Twitter link	Liliana receiving her award for the best pitch at the ULLA summer school for her work on paraben metabolism from Dr. Helder Santos. Helsinki June 2019. https://ullapharmsci.org/ulla-summer-school-2019-in-helsinki/ 🦆 Twitter link

Shalenie den Braver accepting her certificate for the Joep van den Berken 2019 thesis award from Prof. dr. Henk van Loveren at the NVT annual meeting in Ede June 2019. NVT meeting 2019 // Joep van den Bercken Prize Thesis: Inter-individual variation in hepatic drug metabolism 🦆 Twitter link	Robin Coosen accepting the 2019 Bachelor Pharmaceutical Sciences poster award from Chris Vos. Chemistry and Pharmaceutical Sciences 🦆 Twitter link

Projects

The group is a partner in several EU level projects on drug and chemical safety, including EUToxRisk, OpenRiskNet and the recently completed IMI projects StemBANCC and MIP-DILI.

News: Anja has a new project on matrigel replacement, funded by Stiftung zur Förderung der Erforschung von Ersatz- und Ergänzungsmethoden zur Einschränkung von Tierversuchen (set). Read more here.

MolTox Duckery

MolTox logo explained (drawn by the the talented Sam McCabe).

The logo symbolises the ability to model from biological data (the blue liver shaped centre) - in order to expand / fly to new heights of knowledge. The logo also represents the aquatic based habitat of Amsterdam.

We hope you don't think we are quackers.

In between lockdowns - MolTox members kyaking on our lab excursion July 2020, Amsterdamse Bos.

http://moltox.chem.vu.nl https://www.aimms.vu.nl/

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