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
Rosa Luirink
Cormac Murphy
Giada Carta
Liliana Capinha
Vidya Chandrasekaran
Kasia Lazarska
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


All PublicationsLink ]

Recent publications

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1–Ligand Binding Free Energy Calculation Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Arry Yanuar and Daan P. Geerke.
Chem Inf Model. 2019 Sep 23; 59(9): 4018–4033. PMCID: PMC6759767 PMID: 31461271

Characterization of kinetics of human cytochrome P450s involved in bioactivation of flucloxacillin: inhibition of CYP3A- catalysed hydroxylation by sulfaphenazole.  Stefan J Dekker, Floor Dohmen, Nico P E Vermeulen and Jan N M Commandeur.
Br J Pharmacol. 2019 Feb;176(3):466-477.

Function, essentiality, and expression of cytochrome P450 enzymes and their cognate redox partners in Mycobacterium tuberculosis: are they drug targets? Sandra Ortega Ugalde, Maikel Boot, Jan N. M. Commandeur, Paul Jennings, Wilbert Bitter and Chris Vos.
Appl Microbiol Biotechnol. 2019 May;103(9):3597-3614.

Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model. Koen M. Visscher and Daan P. Geerke.
J Chem Theory Comput. 2019 Mar 12;15(3):1875-1883. doi: 10.1021/acs.jctc.8b01105.

awards Higlights
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