Division of Molecular and Computational Toxicology

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

Some of the members of the division as of February 2019. Location O2 Building, Amsterdam. From Left to Right, Chris Vos, Liliana Capinha, Jan Commandeur, Anja Wilmes, Arthur Choy, Paul Jennings, Cormac Murphy, Floor Dohmen, Tamara Meijer, Eko Rifai, Koen Visscher, Sandra Ortega Ugalde, Giada Carta, Ruthmila Paskel, Jessica Moser and Ellen Langemeijer.

The Division of Molecular and Computational Toxicology is specialised in developing computational and 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;
(3) Computational methods for metabolism prediction and data integration.

The laboratory is specialised in analytical chemistry, cell culture, toxicity determination and omic analysis. 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 ]

  • November 25th 13:00 Aula VU: Symposium Animal-Free Innovations in Science. @ 13:40 Paul Jennings: Why we use animals as models for humans and why we might not need to in the future. Please register here (its free and there will be drinks and snacks).
  • December 12th 09:45 Aula, VU: Eko Rifai PhD defence, Applicability and performance of linear interaction energy based binding affinity calculation.
  • January 20th 13:45 Aula VU: Sandra Ugalde, A new target for an old enemy: The Cytochrome P450 system from Mycobacterium tuberculosis.

  • Team
    Senior Scientific Staff PhD Students
    Prof. Dr. Paul Jennings (chair)
    Dr. Jan Commandeur
    Dr. Daan Geerke
    Dr. Chris Vos
    Dr. Anja Wilmes
    Dr. Marc van Dijk
    Dr. Ellen Langemeijer

    Former chair: Prof. dr. Nico Vermeulen

    Technicial Staff

    Ruthmila Paskel
    Daniel Da Costa Pereira

    Floor Dohmen

    Eko Rifai
    Koen Visscher
    Rosa Luirink
    Cormac Murphy
    Giada Carta
    Liliana Capinha
    Sandra Ortega Ugalde
    Vidya Chandrasekaran
    Kasia Lazarska

    Recently completed:

    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 Awards

    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.

      OpenRiskNet      in3logo       EU-ToxRisk
         Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Inju         Welkom bij het NWO   

    MolTox Duckery
    MolTox has a new logo. Thanks to 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