PhD projects in TargetRNA

DC 1: AI-guided design of preQ1-II and SAM-III riboswitch ligands

• Research field: Computational Chemistry, Molecular Simulation, Generative Drug Design.
• PhD candidate: Gaia Dolcetti
• Main Supervisor: Christian Tyrchan
• Host institute: AstraZeneca, BioPharmaceuticals R&D, Research and Early Development, Respiratory & Immunology, Medicinal Chemistry, Gothenburg, Sweden
• Secondments planned: IIT, Molecular Modeling & Drug Discovery Lab, Genova, Italy and UiB, Brenk Lab, Bergen, Norway.
• Doctoral program: Doctoral education at the Faculty of Medicine, University of Bergen. Doctoral education at the Faculty of Medicine | Faculty of Medicine | UiB

PhD project description:

The chemical structures of known ligands and discovered hits within this project will serve as input for AI-guided compound design. We will utilize ReInvent to optimize the identified ligands, employing active learning, docking and free energy calculations. To steer the AI toward desired chemical structures possessing advantageous physico-chemical and biological properties, we will closely collaborate within the project to develop relevant machine learning models (QSA/PR). Novel compounds and their proposed binding modes will undergo further investigation via MD simulations. Evaluation of feasibility and the development of new MD protocols will involve examining the stability of known riboswitches. Subsequently, the stability of the proposed RNA-compound complex will be assessed and specifically refining the binding site and binding mode for compound design.

DC 2: Fragment-based ligand discovery for the preQ1-II and SAM-III riboswitche

• Research field: Fragment-based ligand discovery, organic chemistry.
• PhD candidate: Marta Rosaia
• Supervisor: Prof. Mads H. Clausen
• Host institute: Department of Chemistry, Technical University of Denmark, Denmark
• Secondments planned: Saverna Therapeutics AG, Switzerland.
• Doctoral program: Chemistry at the Technical University of Denmark 

PhD project description:

This PhD project will focus on the identification of small molecules capable of binding to and inhibiting two bacterial riboswitches, preQ1-II and SAM-III. The workflow will consist of NMR screening, hit validation, fragment-to-lead chemistry, and functional validation of lead candidates. The PhD student will work in an interdisciplinary environment where synthetic and medicinal chemistry, cell biology, and animal studies are used for chemical biology and early drug discovery projects. You will have opportunities to work with other scientists within and outside the TargetRNA doctoral network and to collaborate with and supervise undergraduate students.

DC 3: Discovery of recruiters of bacterial endoribonucleases

• Research field: assay development, HTS, organic chemical synthesis, protein expression.
• PhD candidate: Nicolò Mercorelli
• Supervisor: Prof. Mads H. Clausen
• Host institute: Department of Chemistry, Technical University of Denmark, Denmark
• Secondments planned: MUSA, Germany, 4 months: expression and purification of bacterial RNases
• Doctoral program: Chemistry at the Technical University of Denmark

PhD project description:

This PhD project will focus on the identification of small molecules capable of recruiting and activating bacterial endoribonucleases. The training will include protein expression, assay development, high-throughput screening, as well as chemical synthesis of putative RNA degraders. The PhD student will work in an interdisciplinary environment where synthetic and medicinal chemistry, cell biology, and animal studies are used for chemical biology and early drug discovery projects. You will have opportunities to work with other scientists within and outside the TargetRNA doctoral network and to collaborate with and supervise undergraduate students.

DC 4: Hit discovery and structural studies of riboswitch-ligand complexes using NMR and X-ray crystallography

• Research field: Structural biology, NMR spectroscopy, X-Ray crystallography.
• Supervisor: Prof. Charlotte H. Gotfredsen.
• Host institute: Department of Chemistry, Technical University of Denmark, Denmark.
• Secondments planned: Malvern, United Kingdom, 2 months: fragment-screening using GCI; CrystalFirst (Industry, DE), 4 months: crystallographic fragment screening.
• Doctoral program: Chemistry at the Technical University of Denmark

PhD project description:

This PhD project will focus on using NMR spectroscopy for the characterization of the structure and dynamics of two riboswitches in complex with small molecule ligands. Further, different biophysical screening modalities will be compared for the identification of fragment hits for RNA targets. The PhD student will work in an interdisciplinary environment where NMR spectroscopy is used to address structural, dynamic, and metabolomic data from different sources such as chemical, biochemical, or other natural systems. You will have opportunities to work with other scientists within and outside the TargetRNA  doctoral network and to collaborate with and supervise undergraduate students.

Research environment:

The laboratory of Assoc. Prof. Charlotte H. Gotfredsen focuses on NMR spectroscopy for multiple uses in chemical biology and biological chemistry. The group carries out projects where NMR spectroscopy is used as the main analytical technique within RNA structure determination, secondary metabolite structure determination and in situ metabolomic studies as well as NMR based FBDD screening. Furthermore, we work with new developments within NMR spectroscopy both software for metabolomic data deconvolution and alignment media enabling the extraction of long-range NMR structural parameters.
You can read more about DTU Chemistry at www.kemi.dtu.dk/english and more about the CHG group and the NMR Center DTU at www.kemi.dtu.dk/chg

Application to the position:

PhD in MSCA doctoral network: Hit discovery and structural studies of riboswitch-ligand complexes using NMR and X-ray crystallography - DTU Chemistry - DTU Career Site Careers

Application deadline 2 April 2025 (23:59 Danish time).

DC 5: Microbiome Research with a Bioinformatic Focus

• Research field: Molecular microbiology, bacterial physiology
• PhD candidate: Katharina Pütz
• Supervisor: Sebastian Scheich
• Host institute: University Hospital Frankfurt, Germany
• Secondments planned: Matthias Mack, Mannheim, Germany
• Doctoral program: The Goethe Research Academy for Early Career Researchers. 
  Goethe-Universität — Goethe Research Academy for Early Career Researchers (goethe-university-frankfurt.de)

PhD project description:

The aim of the project within the consortium is to study microbiota changes upon administration of compounds active against riboswitches and novel small molecules developed in other project parts in the consortium. In a first step, existing riboswitch active compounds, e.g. for the FMN riboswitch (the non-natural ligands roseoflavin or ribocil) will be tested in vivo in the complex and bacterially diverse microbiome to set a proof of concept that modulation of the gut microbiome by riboswitch modulators is feasible. To do so, the 16S rDNA-sequencing based pipeline to study the microbiome will be complemented by establishing shotgun metagenomics sequencing in a microbiome mouse model. In a second step, an indicator E. coli strain will be utilized and spiked into the microbiome by faecal microbiota transfer to test on target-activity of FMN riboswitch modulators. In a last step, the antibiotic activity of novel riboswitch modulators as single agents and in combination derived from other project parts within the consortium will be tested in vivo to elucidate their impact on the microbiota composition and determine their in vivo activity. Additionally, general toxicity measurements as well as immune profiling is planned to closely monitor side effects.

DC 6: Characterization of riboswitch-ligand interactions using NMR spectroscopy and other biophysical methods

• Research field: NMR of RNA-ligand complexes
• PhD candidate: Olha Vashchenko
• Supervisor: Harald Schwalbe
• Host institute: Goethe University Frankfurt, Germany
• Secondments planned: Malvern, UK and Saverna, Switzerland
• Doctoral program: The Goethe Research Academy for Early Career Researchers. Goethe-Universität — Goethe Research Academy for Early Career Researchers (goethe-university-frankfurt.de)

PhD project description:

The PhD candidate will conduct RNA preparation suitable for fragment screening for the SAM-I/IV riboswitch using NMR at the Schwalbe group. Complementary fragment screening will be conducted by GCI at Malvern. To guide fragment optimization, a second-site screening at Saverna will be conducted. Further, virtual screening hits and newly synthesized compounds from the ITN consortium will be analysed. For selected ligands, more extensive NMR characterisations will be conducted. Specifically, binding sites will be structurally characterised using isotope-labelled riboswitch samples for resonance assignment as well as NOE-filter experiments. In favourable cases, the structure of the ligand-riboswitch complex will be determined. The NMR focused characterisation will be cross validated by other biophysical technologies including CD spectroscopy and SAXS. In addition, the PhD candidate will contribute to the development of in vitro transcription assays for all riboswitches and the 5’-UTR of ompA using previously established methods to determine the activities of compounds discovered in the ITN consortium.

DC 7: Design of compounds targeting the group II intron of Enterobacteriales and Candida

• Research field: Molecular Modeling and Simulations, Computer-Aided Drug Design.
• PhD candidate: Jiangli Gui
• Supervisor: Marco De Vivo
• Host institute: Fondazione Istituto Italiano di Tecnologia, Italy
• Secondments planned: AstraZeneca Sweden
• Doctoral program: PhD Programmes attendance at the University of Bologna. 
  PhD details - Biotechnological, Biocomputational, Pharmaceutical and Pharmacological Sciences — University of Bologna (unibo.it)

PhD project description:

PhD project description: The candidate will make use of equilibrium and enhanced sampling molecular dynamics simulations to investigate the landscape of the group II introns and potential new ligands. Structure-based and computer-aided approaches will be used to rationally drive the design compounds targeting RNA. Physico-chemical properties of the compounds will be computationally evaluated, like solubility and stability measures, to select the best compounds.

DC 8: Mode of action studies

• Research field: Molecular microbiology, bacterial physiology.
• PhD candidate: Lena Winter
• Supervisor: Matthias Mack.
• Host institute: Institute for Technical Microbiology, MUAS.
• Secondments planned: GUF, Frankfurt, Germany (3 months), genome sequencing of resistors; UiB, Bergen, Norway (2 months), surface plasmon resonance experiments to characterize riboswitches.
• Doctoral program: The “Promotionsverband” is an organization of the state of Baden-Württemberg (Germany)

PhD project description:

The PhD project will focus on the in vivo characterization of highly specialized genetic elements, bacterial riboswitches. To monitor the biological activity of various riboswitch ligands in cellulo reporter gene assays (employing different bacterial hosts) will be used. Suitable genetic elements must be assembled in plasmid vectors and coupled to a dual luciferase-based test system. The assays will be employed to investigate whether (novel) RNA ligands indeed interfere with gene expression in a dynamic riboswitch system. The experiments will be complemented by SPR studies at UiB.

Further, the antimicrobial activities of the compounds from other working packages will be tested on different target microorganisms (E. faecalis, E. faecium, S. salvarius, S. anginosus, B. faecis, B. vulgatus, A. baumannii, E. coli, C. albicans, off-target: B. obeum, F. prausnitzii, E. limosum) which will be challenged with different levels and combinations of hit compounds and possible antimicrobials. For the most promising ligands, resistant mutants will be studied in greater detail. Whole genome sequence analysis of these resistors will validate the mode of action of the hit compounds (GUF secondment). Sequence analysis employing state-of-the-art data science tools will help us to study possible off-target effects of the hit compounds. If needed to rationalize the data, we will measure compound uptake into target cells using mass spectrometry.

Finally, an indicator E. coli strain for fecal microbiota transplants in vivo will be developed based on the existing reporter gene assays allowing the monitoring of RNA ligands in a microbiome model (secondment GUF).

The candidate is expected to co-supervise MSc-students and participate actively in professional activities within the TargetRNA network, the research group and the Department of Biotechnology. 

DC 9: Methods to study ligand-RNA target engagement in cellulo

• Research field:
• PhD candidate: Agust Siregar
• Main Supervisor: Willem A. Velema
• Host institute: Department of Physical-Organic Chemistry, Radboud University, Netherland
• Secondments planned: UiB, supervisor Haug, to test the RNA-seq pipeline on covalent ribocil analogues
• Doctoral program: Department of Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University (Netherland) (https://www.ru.nl/en/imm/education/graduate-school)

Project Description: 

The PhD project will focus on the development of a suite of new methods that will enable quantifying specific interactions between small molecule drugs and the RNA targets of interest. A special focus for the PhD candidate will be on assessing the ligand selectivity (that have been established in WP1 and WP2) against tRNA and dsRNA, assessing the binding of covalent modulator using Mass Spectrometry (MS) and Primer Extension Assays, and evaluate the ability of optimized BacRIBOTAC and group II intron inhibitors in degrading the RNA target using qPCR and RNA-seq.

DC 10: Lead finding and structural characterization of the 5’-UTR of ompA of A. baumannii using fragment screening and application of paramagnetic NMR restraints

• Research field: (paramagnetic) NMR, organic synthesis, RNA, structure determination, machine learning, fragment based screening.
• PhD candidate: Sviatlana Kashyrskaya
• Supervisor: Daniel Häussinger
• Host institute: Department of Chemistry, University of Basel, Switzerland
• Secondments planned: Uppsala University structure determination using cryo-EM.
• Doctoral program: Doctoral Studies University of Basel.
  Doctoral Studies | University of Basel (unibas.ch)

PhD project description:

First, we will apply the fragment-based NMR screening method to the 5’-UTR of ompA (at Saverna). For hit expansion, we will use AI methods developed at Saverna to select compounds from large combinatorial compound libraries which will subsequently be tested for binding to the target RNA. The same method will also be used to select follow-up compounds of fragment hits for the remaining targets in the network.

Second, we will determine the structure of 5’-UTR of ompA. The target consists of 131 nucleotides and contains several secondary structure elements. To determine the structure of such a large RNAs in solution by NMR spectroscopy we will develop new methods using paramagnetic restraints. This will also require to synthesize new paramagnetic tags and conjugate them to fragments and/or RNA to refine the RNA-ligand interactions. The obtained PCS will provide long-range (>100 Å) distance and angular restraints that will be very helpful in connecting the secondary structure elements and determine the overall 3D structure of the RNA.

Subsequently, we will probe the influence of ligands developed in WP2 on the dynamics of the target using NMR spectroscopy. We will also collaborate with DC14 on compound design for this target.

DC 11: Design, synthesis and biological evaluation of RNA ligands targeting the SAM-I/IV riboswitch

• Research field: Synthetic small molecules for targeting riboswitch RNA.
• PhD candidate: Elena Mencarelli
• Supervisor: Maria Duca.
• Host institute: University Côte d’Azur (UniCA), France.
• Secondments planned: MUAS, Germany.
• Doctoral program: Fundamental and Applied Sciences (SFA) (https://adum.fr/as/ed/sfa/home.pl)

PhD project description:

The SAM-I/IV riboswitch belongs to a class of riboswitches that specifically binds to S-adenosylmethionine (SAM), a cofactor used in many kinds of methylation reactions. During the development of the project, in collaboration with DC12 and 13, we aim to perform the structure-based design of new ligands specific for this riboswitch using the available crystal structures and the structures determined in WP1 as well as taking advantage of the different analogues of SAM available in the literature for other scopes in addition to the hits discovered here. We will perform the synthesis of different series of RNA binders bearing suitable physico-chemical properties for prokaryote targeting and evaluate their affinity and selectivity using fluorescence-based biochemical assays available in the laboratory (the latter will also be done for other RNA targets). To determine selectivity, we will also measure ligand binding to tRNA and double stranded DNA. The biological evaluation of the most promising compounds in vitro will then be performed during secondments at MUAS and in collaboration with DC8 and DC9. We thus expect to obtain active compounds suitable for further lead optimization but also to increase our knowledge about RNA targeting and biological function thanks to these important chemical biology tools.

DC 12: Characterization of RNA-ligand interactions using X-ray crystallography and other biophysical methods

• Research field: structural biology, biophysics.
• PhD candidate:  Gideon Holzmann
• Supervisor: Ruth Brenk.
• Host institute: Department of Biomedicine, University of Bergen, Norway.
• Secondments planned: CrystalsFirst, supervisor Glinca, establishment of conditions to obtain stable crystals for soaking at high concentration, fragment screening (12 months).
• Doctoral program: Doctoral education at the Faculty of Medicine, University of Bergen. 
  Doctoral education at the Faculty of Medicine | Faculty of Medicine | UiB

PhD project description:

The PhD project will focus on the characterization of RNA-ligand interactions using X-ray crystallography and other biophysical methods to underpin the design of potent RNA-ligands for various targets. In addition, you will also carry out fragment screening using X-ray crystallography to discover new RNA-ligands that can be optimized into compounds with antibiotic activity.

In one part of the work, you will focus on obtaining crystals of the FMN, SAM-III and SAM-I/IV riboswitches suitable for soaking ligands at high concentrations. For this, you will make use of technology developed at CrystalsFirst. CrystalsFirst’s SmartSoak-technology offers a rational process to determine conditions in which macromolecular crystals are stable against the exposure to organic solvents and cryo-protection. Based on these conditions, soaking systems amenable to high concentrations of ligands and long soaking times can be proposed, usually leading to a higher success rate and better resolution than commonly used approaches of trial and error. Subsequently, the established conditions will be used to conduct a fragment screen using X-ray crystallography for the SAM-III and SAM-I/IV riboswitches. In addition, the established conditions will also be used to soak fragment hits obtained in WP2 by other PhD candidates using other technologies. The obtained structures will be fed into WP2 as basis for compound design. Likewise, co-crystal structures of the FMN, SAM-III and SAM-I/IV riboswitches with ligands synthesized in WP2 will be determined to support optimization. 

Further, you will determine binding affinities and binding kinetics of compounds from WP2 for all riboswitches that the consortium will work on and the 5’-UTR of ompA using surface plasmon resonance (SPR). In addition, for selected ligands, you will determine thermodynamic parameters using isothermal titration calorimetry (ITC) to underpin structure-activity relationships (SAR).

DC 13: Virtual screening and design of riboswitch ligands

• Research field: molecular modelling, chemoinformatics, computational chemistry
• PhD candidate: Abdelhamid Mohamed Aboulnaga
• Supervisor: Ruth Brenk.
• Host institute: Department of Biomedicine, University of Bergen, Norway.
• Secondments planned: CrystalsFirst, supervisor Glinca, scaffold-based exploration of chemical space (3 months), LiU, supervisor Pearce, work on and with PanDDA (3 months).
• Doctoral program: Doctoral education at the Faculty of Medicine, University of Bergen. Doctoral education at the Faculty of Medicine | Faculty of Medicine | UiB

PhD project description:

The PhD project will focus on using computational methods for hit discovery for the SAM-III, SAM-I/IV and FMN riboswitches. In particular, you will carry out structure-based virtual screening of ultra-large chemical libraries and chemical spaces containing millions to billions of compounds. Further, you will optimize the hits discovered by virtual screening and fragment screening (WP2) by designing analogues. The compounds will be either purchased or synthesised and tested for binding by fellow students.

Further, our collaborator Nicholas Pearce has developed software that allows analysing data resulting from crystallographic fragment screening (PanDDA). In collaboration with him, you will expand the PanDDA capabilities, so that also RNA crystals can be processed. You will subsequently apply this tool to analyse the crystallographic fragment screening data obtained in the TargetRNA network.

DC 14: Design and synthesis of ligands for the FMN riboswitch and the 5’-UTR of ompA

• Research field: organic synthesis, medicinal chemistry.
• PhD candidate: Daniel Hauken
• Supervisor: Bengt Erik Haug.
• Host institute: Department of Chemistry, University of Bergen, Norway.
• Secondments planned: Marco De Vivo, Italy. 3 months to learn molecular modelling to facilitate design of improved ligands.
• Doctoral program: Doctoral education at the Faculty of Mathematics and Natural Sciences, University of Bergen. 
  Our doctoral education (PhD) | Faculty of Mathematics and Natural Sciences | UiB

PhD project description:

The PhD project will focus on the design and synthesis of small organic molecules as novel ligands for two different RNA targets: i) The flavin mononucleotide (FMN) riboswitch, which regulates the expression of genes involved in biosynthesis and transport of riboflavin and is an established druggable target for antibiotics, and ii) The 5’-untranslated region (UTR) of mRNA coding for the outer membrane protein A (ompA), which plays a crucial role in pathogenicity and virulence of Acinetobacter baumanii.

You will take part in the design of novel target compounds for synthesis and will be responsible for the development of synthesis routes, and synthesis of the target compounds. This will be based on compounds that have been identified through either high-throughput screening, fragment-based screening or molecular design by other project members. You will be tasked with developing new synthesis routes and using these to produce compound libraries for the purpose of establishing structure-activity relationships.

You will work in a team together with other synthesis- and medicinal chemists both within the TargetRNA doctoral network and the research group. The work tasks will be varied, and you will be given the opportunity to contribute to developing new solution in a research environment that focuses on innovation. Testing in biochemical assays will be carried out by other project members as well as external partners.

You are expected to co-supervise MSc-students and participate actively in professional activities within the TargetRNA network, the research group and at the Department of Chemistry.

DC15: Establishing a toolbox of warheads for covalent targeting of RNA

• Research field: organic synthesis, medicinal chemistry.
• PhD candidate: Timm Krüger
• Supervisor: Bengt Erik Haug.
• Host institute: Department of Chemistry, University of Bergen, Norway.
• Secondments planned: Willem Velema, The Netherlands. 3 months to learn about RNA labelling to facilitate covalent warhead discovery.

• Doctoral program: Doctoral education at the Faculty of Mathematics and Natural Sciences, University of Bergen. Our doctoral education (PhD) | Faculty of Mathematics and Natural Sciences | UiB

   

PhD project description:

The PhD project will focus on the design, synthesis, and characterization of covalent warheads targeting the 2’OH group in RNA nucleotides to create a broad toolbox to enable the discovery of covalent RNA ligands. Binding parameters will be optimized for both reversible and irreversible covalent binders, including time bound within the RNA, by tuning both steric and electronic properties of the warheads. Synthetic modification of warheads and synthesis of analogues will be essential to drive the discovery forward. The flavin mononucleotide (FMN) riboswitch will be used as model system for validating the warheads. Promising warheads will be appended onto the scaffold of known FMN riboswitch ligands to obtain covalently binding FMN ligands.

You will be responsible for the screening of commercially available candidate warheads and characterization of stability and identity of their adducts. Utilizing identified warheads, you will take part in the design of novel target compounds for synthesis and will be responsible for the development of synthesis routes, and synthesis of the target compounds. You will be tasked with developing new synthesis routes and using these to produce compound libraries for the purpose of establishing structure-activity relationships.

You will work in a team together with other synthesis- and medicinal chemists both within the TargetRNA doctoral network and the research group. The work tasks will be varied, and you will be given the opportunity to contribute to developing new solution in a research environment that focuses on innovation. Testing in biochemical assays will be carried out by other project members as well as external partners.

You are expected to co-supervise MSc-students and participate actively in professional activities within the TargetRNA network, the research group and at the Department of Chemistry.

DC 16: Structural characterization of group II introns from Enterobacterales and Candida species and the 5’UTR of ompA bound to inhibitors using cryo-EM

• Research field: RNA cryoEM, structural biology, RNA biochemistry.
• PhD candidate: Saha Spandan
• Supervisor: Marco Marcia.
• Host institute: Uppsala University, Sweden.
• Secondments planned: IIT Genova, Italy (supervisor: De Vivo), University of Basel (supervisor: Häussinger).
• Doctoral program: PhD studies at Uppsala University. PhD studies - Uppsala University (uu.se)

PhD project description:

We will apply cryo-EM and integrative structural biology and biochemical approaches (X-ray, SAXS) to characterize binding of small molecule inhibitors to bacterial and fungal ribozymes and regulatory UTR regions. We will use cutting edge cryo-EM sample preparation, data acquisition and data processing approaches to capture these small-molecule-bound RNAs at high resolution, visualizing how the compounds impede catalysis and modulate the structural dynamics of the target RNAs. The targets consist of ~400-800 nucleotides and adopt highly structured 3D fold. Useful references: Marcia and Pyle, Cell, 2012; Manigrasso et al, Nat Comm, 2020; Manigrasso et al, Chem, 2021; Martin et al, TIPS, 2021; Silvestri et al, Nat Comm, 2024.