PhD position in structure-based RNA-ligand design - third round advertisement

PhD position in structure-based RNA-ligand design - third round advertisement
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PhD position

At the Faculty of Medicine, Department of Biomedicine in the group of Professor Ruth Brenk (http://www.uib.no/en/rg/brenk ), a PhD-position (100 %) is available for a period of four (4) years or max 4 months after completed the PhD-degree, if this is achieved within a shorter time than four years. 

The position is part of the project “Paving the way for rational RNA-ligand design” financed by The Research Council of Norway

About the project/work tasks:

The vast majority of targets for approved drugs are proteins. In recent years, it has been increasingly realized that also RNA molecules constitute promising targets. However, compared to protein targets, RNA targets are vastly underexplored. By targeting RNA, the functions of currently undruggable protein-mediated pathways and the non-coding transcriptome can be modulated and thus the size of the druggable genome can be increased substantially. A major obstacle in RNA-targeting drug discovery is the lack of knowledge on how to obtain drug-like RNA ligands. The main goal of this project is therefore to establish a blueprint on how to design drug-like, potent, selective, and functional RNA ligands based on the 3D structure of the target and to advance our understanding of what drives potency and selectivity of RNA ligands on the molecular level. Focusing on RNA targets that contain druggable binding site will allow us to transfer methods that are at the forefront in structure-based design in the protein field to RNA. For that purpose, we have chosen two emerging targets for antibiotics, the FMN and TPP riboswitches (genetic switches in bacterial mRNA), as model systems. Hit compounds will be advanced through “design-synthesis-test” cycles and extensively characterized in terms of binding affinity and kinetics, functional activity, selectivity, and binding modes. This will deliver detailed knowledge about RNA-ligand interactions which is crucial to advance RNA-targeted drug discovery. In addition, the project will deliver advanced starting points for antibiotic drug discovery. We anticipate that this study will lead to a paradigm shift in the RNA field away from the currently rather unsuccessful “one size fits all” approach to a more target-centred approach where the nature of the binding site is taken into account.

In this project, two PhD students, one postdoc and one researcher will tightly collaborate on compound design, synthesis and testing.

More information about the project can be found here: https://www.uib.no/en/rg/brenk/162656/paving-way-rational-rna-ligand-design .

The main objectives for the advertised PhD position are

• to carry out structure-based design of RNA-ligands
• to establish computational methodology on how to harvest the potential of large, chemically accessible combinatorial spaces for the design of RNA ligands
• to determine the binding affinities of RNA ligands
• to determine the crystal structures of RNA-ligand complexes

This PhD project will be conducted in collaboration with the group of Prof. Jens Carlsson at Uppsala University in Sweden implying that this position will involve research stays in his lab.

Qualifications and personal qualities:

• The applicant must hold a master`s degree or equivalent within the field of cheminformatics, bioinformatics, pharmacy, medicinal chemistry, or a related discipline, or must have submitted his/her master's thesis for assessment prior to 30th of June 2024. It is a condition of employment that the master's degree has been awarded.
• The applicant must have a thorough understanding of structure-based ligand design.
• Basic knowledge of a scripting language is required.
• Experience with RDKit is a distinct advantage.
• Experience with modelling RNA structures or RNA-ligand interactions is a distinct advantage.
• Training in organic synthesis or medicinal chemistry is a distinct advantage.
• Experience with using biophysical methods for determination of binding affinities is a distinct advantage
• Experience in X-ray crystallography is a distinct advantage.
• The candidate must demonstrate a strong commitment and enthusiasm for structure-based drug design of RNA-ligands and for research in general. The candidate must be able to work independently and interactively in a team setting. A structured approach to work and excellent communication skills and fluency in both written and spoken English are required.

Language qualifications: http://www.uib.no/en/med/115526/english-language-requirements-phd-admission .

About the PhD position (applies to university PhD positions):

The duration of the PhD position is 4 years, of which 25 per cent of the time each year comprises required duties associated with research, teaching and dissemination of results. The employment period may be reduced if you have previously been employed in a recruitment position.

The candidate must take part in the University of Bergen approved PhD programme leading to the degree within a time limit of 3 years. You must have admission to the organized research training (PhD program) at the Faculty in order to qualify for the position.

Application for admission to the PhD programme, including a project plan outline for the training plan must be submitted no later than three months after the date of commencement.

PhD-positions are fixed term positions. You cannot be employed in a PhD-position for more than one fixed term period at the same institution or have had similar employment at an institution in the region.

We can offer:

• Exciting development opportunities as part of your role in a strong professional environment
• Salary at pay grade 55 (code 1017/pay framework 20.10) NOK 540 500 before taxes, in the state scales. Further increases in salary will be based on seniority in the position.
• Enrolment in the Norwegian Public Service Pension Fund
• Good welfare benefits

Your application must include:

• A brief account of the applicant`s research interests and motivation for applying for the position

• Certified copies of diplomas and transcripts of grades. Applicant whose education is from another country than Norway, need to also attach a certified translation of the diploma and transcript of grades to English or a Scandinavian language, if the original is not in any of these languages. It is also required that the applicant enclose a review from HK-dir (both bachelor and master degree) whether the education in question is of a scope and level that corresponds to the level of a Norwegian master’s degree. Please see https://hkdir.no/en/ for more information about HK-dir’s general recognition. This may take some time and we recommend you to apply as soon as you know you will apply for this position. If no answer within the application deadline, please enclose documentation from HK-dir that they have received your application

• Documentation of language skills (English)

• Complete list of publications and scientific work you want to be evaluated

• Any publication in your name

• Two references (name and contact information

General information:

Detailed information about the position can be obtained by contacting professor Ruth Brenk, e-mail: [email protected].

Diversity is a strength that enables us to solve our tasks even better. UiB therefore needs qualified employees regardless of gender, ethnicity, religion, worldview, disability, sexual orientation, gender identity, gender expression, and age.

The University of Bergen applies the principle of public access to information when recruiting staff for academic positions.

Information about applicants may be made public even if the applicant has asked not to be named on the list of persons who have applied. The applicant must be notified if the request to be omitted is not met.

The successful applicant must comply with the guidelines that apply to the position at all times.

We encourage applicants with disabilities, immigrant backgrounds, or gaps in their CV to apply. By indicating such circumstances in your application, you may receive favourable consideration. We ensure that at least one qualified applicant from each of these groups is invited for an interview as part of our commitment to inclusivity and equal opportunity. For further information about the recruitment process, click here .

Life as a PhD candidate at UiB

Marion Claireaux tells about life and work as a PhD candidate at UiB.

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About UiB

The University of Bergen is a renowned educational and research institution, organised into seven faculties and approximately 54 institutes and academic centres. Campus is located in the centre of Bergen with university areas at Nygårdshøyden, Haukeland, Marineholmen, Møllendalsveien and Årstad. 

There are five departments and eight centres at Faculty of Medicine.

Read More about the facult y and departments .

 

Questions about the position

Ruth Brenk

Professor

[email protected]

Apply for this job
Deadline

21st May 2024

Employer

University of Bergen

Municipality

Bergen

Scope

Fulltime (1 positions) Fulltime (%)

Duration

Fixed Term

Place of service
Jonas Lies vei 91, 5021 Bergen

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