PhD position: Computer-Aided Drug Design of GPCRs ligand

Updated: 7 months ago
Deadline: ;

Do you have experience in computer-aided drug design and are you interested developing and applying these approaches in the area of G-protein Couple Receptors? Then we would like to get to know you. Please apply at Vrije Universiteit Amsterdam.

FTE: 1 - 1 

Job description

This PhD project will focus on structure- and ligand-based design of GPCR modulators. You will develop and apply new computational techniques to design and optimize modulators of the GPCRs targets that are being studied in our division. Multidisciplinary team work will allow for the iterative process of computational prediction, organic synthesis and pharmacological validation of new compounds. The PhD candidate will be surrounded by an expanding CADD group and the vibrant multi-disciplinary medicinal chemistry environment.

Your duties

  • Analyze the literature to understand the current trends in the field of GPCRs
  • Perform cheminformatic studies to capture and process available ligand-protein interaction data
  • Apply various techniques (homology and pharmacophore modelling, QSAR, Virtual Screening, FEP+ etc.) to facilitate small molecule synthesis
  • Closely collaborate with medicinal chemists and pharmacologists to develop new tool compounds and/or support hit to lead campaigns
  • Write scientific publications

  • a Master's degree in (Medicinal) Chemistry, Bioinformatics, or related field
  • Experience in molecular modelling of GPCRs and enzymes is required 
  • Experience in a variety of computational techniques such as homology modelling, pharmacophore modelling, docking, virtual screening is required
  • Experience in Molecular Dynamics studies would be an advantage
  • Experience in free energy perturbation is required
  • Experience in the application of AI/ML methods to drug discovery would be an advantage
  • Experience in programming, scripting and bioinformatics would be an advantage
  • Strong collaboration and communication skills in writing and speaking

What are we offering?

A challenging position in a socially involved organization. The salary will be in accordance with university regulations for academic personnel and amounts €2,395 per month during the first year and increases to €3,061 per month during the fourth year, based on a full-time employment. The job profile: promovendus, is based on the university job ranking system and is vacant for at least 1 FTE. The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of in total 4 years.

Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:

  • 8% holiday allowance
  • 8.3% end-of-year bonus
  • contribution to commuting expenses
  • a wide range of sports facilities which staff may use at a modest charge

About Vrije Universiteit Amsterdam

The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. We strive to be a university where personal development and commitment to society play a leading role. A university where people from different disciplines and backgrounds collaborate to achieve innovations and to generate new knowledge. Our teaching and research encompass the entire spectrum of academic endeavour – from the humanities, the social sciences and the natural sciences through to the life sciences and the medical sciences.

Vrije Universiteit Amsterdam is home to more than 26,000 students. We employ over 4,600 individuals. The VU campus is easily accessible and located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.

We are an inclusive university community. Diversity is one of our most important values. We believe that engaging in international activities and welcoming students and staff from a wide variety of backgrounds enhances the quality of our education and research. We are always looking for people who can enrich our world with their own unique perspectives and experiences.

The Faculty of Science
The Faculty of Science inspires researchers and students to find sustainable solutions for complex societal issues. From forest fires to big data, from obesity to medicines and from molecules to the moon: our teaching and research programmes cover the full spectrum of the natural sciences. We share knowledge and experience with leading research institutes and industries, both here in the Netherlands and abroad.

Working at the Faculty of Science means working with students, PhD candidates and researchers, all with a clear focus on their field and a broad view of the world. We employ more than 1,250 staff members, and we are home to around 6,000 students.

About the department, institute, project
The division has two main research lines, G protein-coupled receptors (GPCRs) and Fragment-Based Drug Discovery. Within the GPCR research line, the division has been focusing especially on histamine receptors and chemokine receptors. The computational group uses the rapidly emerging structural understanding to develop GPCR activation models, construct ligand-protein binding models, deduce structure-activity relationships and to identify and optimize novel GPCR ligands. Within the fragment-based drug design research line, molecular modelling explores a variety of protein classes, including GPCRs, phosphodiesterases and ligand-gated ion channels. Identification of fragment hits is followed up by structure-based drug design to develop potent lead compounds with favourable pharmacodynamic and pharmacokinetic properties. Fragment-based approaches are also used to study fundamental aspects of ligand-protein binding, especially with respect to affinity, binding kinetics and thermodynamics, using experimental data that is generated by a variety of techniques, including biochemical and biophysical screening such as SPR, ITC and x-ray crystallography. Bio- and cheminformatics approaches are being used to study poly-pharmacology as a promising approach to develop new drug candidates with clinical potential (especially in the field of neglected parasitic diseases and inflammation).

This position fills a vacant role in the Computational Chemistry group, which is an integral part of the Medicinal Chemistry division. Importantly, the Medicinal Chemistry Division has extensive research experience in GPCRs field and has large academic and industrial collaborations.


Are you interested in this position? Please apply via the application button and upload your curriculum vitae and cover letter until

October 15, 2020. 

Applications received by e-mail will not be processed.

Vacancy questions
If you have any questions regarding this vacancy, you may contact:

Name: Prof. Iwan de Esch or Dr. Barbara Zarzycka

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