What is TargetRNA about
TargetRNA is a MSCA doctoral training network. In total, 16 doctoral candidates will work together across different disciplines to jointly advance the field of RNA-ligand design.
Main content
In recent years it became increasingly evident that RNAs constitute promising macromolecular drug targets for small molecule drugs. By targeting upstream RNA, current undruggable protein-mediated pathways could be effectively modulated thereby opening for innovative therapies that my redefine the treatment strategies for a range of conditions. However, to advance this field of research, a new generation of scientists that can further develop and ultimately master the challenging process of drug design applied to RNA molecules is needed. Therefore, the TargetRNA network aims to educate and nurture the next generation of scientists with cutting-edge interdisciplinary skills in the discovery and biological characterization of RNA modulators and thus generate fundamental knowledge on what drives affinity and specificity of small molecules binding to RNA. Here, we will focus on developing antimicrobial tool compounds to selectively reshape the human gut microbiome by targeting RNA, an area with vast implications for medicine. Training through research activities, spanning from computational and medicinal chemistry over structural and molecular biology to microbiology and in vivo models, will be supplemented by an innovative training program in specific and transferable skills for interdisciplinary drug discovery strategies to target RNA, including FAIR data principles, open science practices as well as responsible development and sustainable implementation of new innovations. To achieve the ambitious research and training goals, the TargetRNA network unites leading scientists from 13 academic partners (8 beneficiaries, 5 associated) and 4 industry partners (1 beneficiaries, 3 associated) based in 9 countries.
To structure the project, it has been devided into 5 work packages (WPs).
Work package structure of TargetRNA.
WP 1: Structural biology of RNA targets
Objectives:
- Determine the structures of RNA-ligand complexes using NMR, X-ray crystallography, and cryo-EM;
- Evaluate the dynamics of the binding pocket, impacted by ligand binding using NMR;
- Establish robust crystallization conditions and processing pipelines to enable fragment screening by X-ray crystallography.
WP leader:
Charlotte Gotfredsen (DTU)
Description of Work and Role of Specific Beneficiaries / Associated partners
The aim and tasks of this WP are focused on gaining structural knowledge on the RNA-ligand interactions, what the impact of ligand binding on the binding pocket conformation and the overall structural fold is, and how this knowledge can guide the design of new ligands with increased binding affinity and specificity. UiB will focus on the FMN, SAM-I/IV, and SAM-III targets using X-ray crystallography. GUF will focus on the SAM-I/IV riboswitches, mainly using NMR spectroscopy. UU will focus on the group II intron ribozyme using X-ray crystallography and cryo-EM. DTU will be using mainly NMR spectroscopy to investigate the binding, specificity and dynamics between promising fragments as well as elaborated ligands on the two targets preQ1-II and SAM-III. The structure of the 5’-UTR of ompA will be determined using NMR (UB) and cryo-EM (UU). CrystalsFirst will broaden the scope of their SmartSoak technology to make it applicable to RNA crystals and we will work with LiU to make PanDDA work with RNA structures, too.
WP 2: Discovery and optimization of RNA ligands
Objectives:
- Identify RNA ligands by experimental screening of fragment libraries using NMR; GCI, and crystallography as well as virtual screening of (ultra-large) chemical libraries and generative AI models;
- Screen for covalent warheads and RNase activators;
- Design potent ligands, including covalent ligands and BacRIBOTACs, using a structure-based approach in combination with AI-active learning strategies;
- Synthesize optimized ligands
WP leader:
Maria Duca (UniCA)
Description of Work and Role of Specific Beneficiaries / Associated partners
The overarching aim of this work package is to discover, design and synthesize new RNA ligands against the chosen targets. CrystalsFirst will conduct fragment-screening using X-ray crystallography, GUF, DTU, and Saverna using NMR, and Malvern using GCI. We will screen proprietary libraries as well as the EU-OS fragment library. UiB will use uLSD and AZ AI-driven de novo design as alternative hit discovery methods. Compounds will be optimized for affinity to the respective RNA targets guided by computational design (AZ, UiB, Saverna, IIT, CrystalsFirst) and exploiting knowledge of their binding modes (WP1). The compounds will be synthesized by UniCA, DTU, IIT, and UiB and tested in WP3 to establish SAR. Further, DTU will conduct a HTS to identify RNase activators and UiB will discover covalent warheads selective for RNA. The activators and warheads will be coupled to potent RNA ligands to develop BacRIBOTACs (DTU, UniCA, UiB) and covalent ligands (IIT, UniCA, UiB).
WP 3: Assay development and biological evaluation
Objectives:
- Identify a suitable RNase for BacRIBOTACs;
- Develop assays to determine binding affinity and functional activity in vitro and in cellulo;
- Determine binding affinity and functional activity in vitro and in cellulo to underpin SAR studies;
- Profile antimicrobial activity of RNA ligands;
- Elucidate effects of novel RNA ligands on the microbiome.
WP leader:
Sebastian Scheich (GUF)
Description of Work and Role of Specific Beneficiaries / Associated partners
The aim of this work package is to develop assays that can be used to understand the effects of RNA ligands in vitro, in cellulo and in vivo. To do so, the binding affinities against the RNA targets will be determined using SPR, ITC (UiB), and fluorescence (UniCA). For assessing the selectivity, the ligands will also be tested against tRNA and double stranded DNA. Binding of covalent modulators will further be assessed using MS and primer extension assays (RU). Optimized BacRIBOTACs and group II intron inhibitors will be evaluated on their ability to degrade/cleave target RNAs using quantitative PCR and RNA-seq (RU). Functional activity in vitro (GUF, UU) and in cellulo (MUAS) and the antimicrobial activity will be determined (MUAS). In a last step, in cellulo validated, active RNA ligands will be tested and the effects on the microbiome will be studied in a mouse model at GUF.
WP 4: Training
Objectives:
- Organization, coordination, and implementation of the training activities
WP leader:
Bengt Erik Haug (UiB)
Description of Work and Role of Specific Beneficiaries / Associated partners
- Organization of network meetings (UiB, GUF, DTU);
- Implementation of the mentoring programme (UiB with input from all);
- Organization of summer school (MUAS, EU-OS);
- Compile personal career development plan (PCDP) and monitor progress through DC logs (all supervisors and DCs);
- Oversee training activities (UiB, MUAS, CrystalsFirst).
WP 5: Dissemination, Communication & Public Engagement
Objectives:
- Coordination and supervision of the dissemination and communication within the network
WP leader:
Wim Velema (RU)
Description of Work and Role of Specific Beneficiaries / Associated partners
- Development of a public engagement and exploitation strategy (RU, UU, EU-OS, Saverna with input from all);
- Organization of a final outreach campaign (RU and all DCs);
- Website (4 DCs);
- Communication of research via social media (4 DCs);
- Participation in open science days and similar events (all DCs);
- Scientific publications and presentations (all);
- Oversee the work of the IP committee
- Transfer or licensing of patents (all)
- 9. COST Action application to continue networking after funding period (UU)
- Donation of non-sensitive compounds to the EACL of EU-OS compound collection (IIT, UniCA, UiB, DTU).
WP 6: Management
Objectives:
- Effective coordination of the training, research, and administration of all network-related activities
WP leader:
Ruth Brenk (UiB)
Description of Work and Role of Specific Beneficiaries / Associated partners
- Recruitment (UiB, UB, IIT and all beneficiaries);
- Data Management Plan (all / ELIXIR);
- Risk management (UiB with WP leaders);
- Communication with the European Commission (UiB);
- Conflict resolution (UiB);
- Network finance management (UiB).
