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, 's-Hertogenbosch) and India - via Zoom. [Other group photos]

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.

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 ]

De Team
Senior Scientific Staff PhD Students
Prof. Dr. Paul Jennings (chair)
Dr. Daan Geerke
Dr. Chris Vos
Dr. Anja Wilmes
Dr. Ellen Langemeijer

Dr. Jan Commandeur
Dr. Alice Limonciel
Prof. dr. Nico Vermeulen
Dr. Marc van Dijk

Technical Staff

Daniel Da Costa Pereira
Elisabeth Naderlinger

Project Staff

Emma Scuric

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

Video Section

All PublicationsLink ]

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  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  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  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  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  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  10.1016/

awards Highlights

The group is a partner in several EU level projects on drug and chemical safety, including EUToxRisk, OpenRiskNet and the completed IMI projects StemBANCC and MIP-DILI. Anja has a new project on matrigel replacement, funded by Stiftung zur Foerderderung der Erforschung von Ersatz- und Ergänzungsmethoden zur Einschränkung von Tierversuchen (set). Read more here.

MOMHALK set openrisknet in3logo EU-ToxRisk Welkom bij het NWO

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. 

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