Division of Molecular and Computational Toxicology

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

Some of the members of the division as of March 2020. Location O2 Building, Amsterdam. [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 ]


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

Prof. dr. Nico Vermeulen
Dr. Marc van Dijk

Technicial Staff

Daniel Da Costa Pereira
Elisabeth Naderlinger

Floor Dohmen
Ruthmila Paskel

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 -   Mistaken 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

Assistant professor (tenure track) in xenobiotic metabolism and analytical toxicology.
Apply here:


All PublicationsLink ]

Recent publications

NEW ! 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/


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.

The award was given by Management & Science University (MSU), Malaysia ( In the picture, Prof. Dr. Eddy Yusuf and Eko Rifai.

🦆Link to tweet:

Congratulations to Sandra and Vidya for their AIMMS talk and AIMMS poster prize at the AIMMS day 18th April, 2019.
🦆 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.
🦆 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


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.

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. 

We hope you don't think we are quackers.

MolTox members, preparing for the trees on our lab excursion May 2019, Amsterdamse Bos.                   tweets