Molecular and Computational Toxicology

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.

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

Upcoming

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

Former:
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

Publications

All Publications [ Link ]

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 https://pubs.acs.org/doi/10.1021/acs.jcim.9b00609

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. https://doi-org.vu-nl.idm.oclc.org/10.1111/bph.14548

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. https://doi.org/10.1007/s00253-019-09697-z

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

	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.

Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Inju

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.

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

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