Structure-based design of new GPCR ligands (Postdoc position)

Updated: about 1 month ago

Our studies make computer-aided drug design more efficient, thereby enabling the development of efficient and safe medicines. If you can help us develop and apply computational chemistry directed towards GPCRs then we would like to get to know you. Please apply at Vrije Universiteit Amsterdam.

FTE: 1 - 1

Job description

You will curate GPCR structural information and apply structure-based drug design technologies to develop new chemical biology tools (e.g., photoswitchable ligands) and new biologically active compounds for particular GPCR drug targets (or panels of several GPCR targets). At present, the Computer-Aided Drug Design (CADD) group is rapidly expanding and the candidate will help to accommodate the new undergraduate and graduate students.

Your duties

  • Generate various models (homology, pharmacophore, QSAR, COMFA, etc.) that help us to understand biological activity and guide efficient drug design
  • Participate in the generation and exploration of ideas using cheminformatics tools
  • The developed technologies and molecular understanding should result in high quality publications
  • Contribute to the teaching program of the Medicinal Chemistry Department  (e.g. supervision of Master students)

  • Demonstrated experience in molecular modeling, computational chemistry and cheminformatics applied to drug design campaigns
  • Research experience in one or more of the following areas is essential: structure-based design, pharmacophore modeling, QSAR, 3D database searching, combinatorial library design, cheminformatics, and lead optimization
  • Sound knowledge of at least one of the drug discovery software packages (Molsoft ICM, MOE, Discovery Studio, Schrodinger, OpenEye, KNIME) is required
  • Programming and scripting skills (Linux shell, Python, Perl) is required, additional knowledge of database management is an advantage
  • Experience in free energy perturbation would be an advantage
  • Experience in the application of AI/ML methods to drug discovery is required
  • Demonstrated experience in Molecular Dynamics studies is required
  • Established record of high-quality scientific publications
  • Strong analytical and problem-solving skills are essential
  • Strong and highly effective verbal and written communication skills
  • Highly motivated and self-directed, teamwork-oriented personality
  • Experience in communicating and collaborating effectively with medicinal chemists, structural biologists and other members of cross-functional project teams
  • Ability to work independently and collaboratively in a multidisciplinary, team-oriented environment

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 €2,790 per month up to €4,402 per month depending on experience, based on a full-time employment. The job profile: researcher, is based on the university job ranking system and is vacant for at least 1 FTE. The appointment will initially be for 1 year.

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

  • optional model for designing a personalized benefits package
  • 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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