Assistant Professor in Artificial Intelligence and Structure-Based Drug Discovery

The Faculty of Science and the Leiden Academic Center for Drug Research are looking for a

Assistant Professor in Artificial Intelligence and Structure-Based Drug Discovery (1.0 fte)

Background
Computational methods have grown to be an integral part of drug discovery over the last three decades. Prior to the ongoing AI revolution, computer aided drug discovery (CADD) was already firmly embedded in the drug discovery process. Publicly accessible databases have emerged such as ChEMBL, and DrugBank, which complement the available of prior data sources such as the PDB. This has resulted in the availability of bioactivity data for a massive number of small molecules. In parallel the introduction of AlphaFold 2 and 3 have unlocked the world of structure-based drug discovery with the availability of a massive amount of experimentally and machine learning obtained protein structures.

Moreover, significant increases in computational power (e.g. development of graphics processor unit (GPU)-based computing) have gone hand in hand with the development of innovative algorithms like deep learning. In addition, the increased computational power provided by GPUs is being exploited for more extensive and detailed molecular dynamics (MD) simulations using the unlocked protein structure potential. These developments have sparked a renewed interest in the usage of MD to understand the dynamical processes that underlie ligand binding to proteins. But also, a revival of free-energy perturbation-based approaches as a means to predict the affinity of ligands for a given protein target. Resulting from these methods are large quantities of data describing temporal trajectories of (macro)molecules at an atomistic scale.

The vacancy is in the PI group Computational Drug Discovery (CDD) and in close collaboration with the national growth fund project Oncode Accelerator, specifically the AI platform. CDD works on the intersect between medicinal chemistry and computational sciences and applies novel AI algorithms to chemical and biological data. The group expertise is in combining heterogenous data (including data on mutations and polypharmacology) for predictive modelling. Furthermore, close collaborations are in place with other PI groups allowing synthesis and biological testing of AI designed molecules.

Job Description
Educational program
At LACDR both the BSc program BioFarmaceutische Wetenschappen and the MSc program BioPharmaceutical Sciences (collectively BFW/BPS) are hosted. This position will contain teaching tasks in both curricula. Given the significant increase in the role computational methods are playing in drug discovery, we are adapting the curricula to match. The candidate is expected to develop novel courses, improve existing courses, and supervise internship students.

Research, using AI to improve structure-based methods

A part of the position is focused on research. At the division of Medicinal Chemistry our interest is focused on understanding the interplay between ligands and proteins at an atomistic scale. A significant expertise is available in the area of AI, machine learning, and big data analysis. Future and current research directions are expected to further integrate these methods with MD simulations, the study of data produced by MD simulations, and the application of Free Energy Perturbation based methods. Moreover, and connecting these methods to machine learning (in particular in polypharmacology and proteochemometrics), and large language models is expected

Selection criteria
We are looking for a highly motivated candidate, who has:

• A PhD degree in Pharmaceutical Sciences, Informatics, Computational Chemistry, or related disciplines;
• Affinity with teaching;
• A strong interest and shown experience in machine learning and structure-based drug discovery;
• Experience in python;
• Experience in polypharmacology modeling and proteochemometrics;
• Excellent proficiency in English;
• Collaborative mind set;
• Good technical skills;
• The candidate should feel comfortable working in a collaborative environment. Initiative, creativity and an independent working attitude are highly valued. Planned start date April 2025, or soon thereafter.

Research at our faculty and institute
The Leiden Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. Our people are driven by curiosity to expand fundamental knowledge and to look beyond the borders of their own discipline.

The research carried out at the Faculty of Science is diverse, ranging from artificial intelligence, computer science, mathematics, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The faculty has grown strongly in recent years and now has more than 2,300 staff and almost 5,000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together. For more information, see https://www.science.leidenuniv.nl.

Leiden Academic Centre for Drug Research
Leiden Academic Centre for Drug Research (LACDR) is a centre of excellence for multidisciplinary research on drug discovery and development. Leiden University ranks within the top-20 world-wide within the subject-based QS Ranking in Pharmacology and Pharmacy. At LACDR, we develop innovative scientific concepts in fundamental and translational research underlying the discovery and optimization of drugs, and personalised medicines. We aim to optimise the route to novel drugs that are both efficacious and safe, and therefore our research focuses on drug discovery and safety, bio-therapeutics, and systems biomedicine and pharmacology. State-of-the-art expertise and infrastructures ensure that we are strategically positioned in (inter)national collaborations, thus further strengthening the development of novel concepts and their application in a clinical and industry environment.

Medicinal chemistry combines a molecular understanding of the interaction between small molecules and their protein targets with cheminformatics for development of novel and safe drug leads.

LACDR has close on-going collaborations with the Leiden University Medical Centre (LUMC) and the Centre for Human Drug Research (CHDR). More information about the LACDR can be found at https://www.universiteitleiden.nl/en/science/drug-research.

Terms and conditions
We offer a position for four years (on the basis of 0.8 or 1.0 FTE). Salary ranges from € 4.537,- to € 6.209,- to,- gross per month based on a full-time employment, (pay scale 11 in accordance with the Collective Labor Agreement for Dutch Universities).Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. Candidates from outside The Netherlands may be eligible for a substantial tax break.

Diversity
Diversity and inclusion are core values of Leiden University. Leiden University is committed to becoming an inclusive community which enables all students and staff to feel valued and respected and to develop their full potential. Diversity in experiences and perspectives enriches our teaching and strengthens our research. High quality teaching and research is inclusive.

Information
Inquiries about the research area can be made to Prof. Dr. GJP van Westen, gerard@lacdr.leidenuniv.nl. If you have any questions about the procedure, please contact Nicole van Zaal, n.van.zaal@lacdr.leidenuniv.nl

Applications
To apply for this vacancy, please submit your application online through the blue button below. Please ensure that you upload the following additional documents:
Applications are written in English and include a Cover Letter indicating the motivation for the project (which includes a vision on computational education);

• An updated CV, including a list of publications;
• A copy of your PhD thesis;
• A copy of your PhD degree;
• Contact details of two references, including names, affiliations and email addresses.

Only applications received no later than March 7th 2025 can be considered. The selection procedure will take place in March 2025, and selected candidates may be invited for a remote interview in this period, during which you are kindly requested to be available.

Acquisition in response to this vacancy is not appreciated.

32 - 40 hours per week

Rapenburg 70