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Changing the Dynamics and Structures of key viral RNA structures using nano-size supramolecular drugs
Secondary Supervisor(s): Dr Zania Stamataki
University of Registration: University of Birmingham
BBSRC Research Themes:
Project Outline
RNA structure targeting is a new frontier for molecular design. It offers unique opportunities to gain new understanding of the function of RNAs. Functional RNA structures in untranslated regions (UTRs) of many viruses are intriguing targets. UTRs have functionally essential structural elements that are conserved as the virus evolves genetically. Structure-affecting mutations inactivate the virus. In RNA viruses, such as HIVs, coronaviruses, dengue and zika, functional involvement of the UTR has been shown in initiation of replication (e.g. by recruiting proteins or interaction with the ribosome) or regulation of the replication cycle.
Metallo-supramolecular helicates are unique nano-drugs that bind DNA and RNA cavities - different sizes/shapes target 3-way junctions, 4-way junctions or various bulges [1-2]. The helicates can bind UTR structures in RNA of both HIV and SARS-CoV-2 viruses and prevent their replication in cells [3-5].
This project combines molecular design, biophysics and in-cell study of RNA structures and molecular dynamics simulations to get unique insight into the binding events, their structural effects and effects on RNA dynamics. Biophysical studies will include gel studies, competition assays and RNA SHAPE assessment of binding on viral UTRs. Chemical synthesis and design will be used to prepare the new binding agents.
The approach and understanding developed will create a new roadmap for design of drugs to target RNA structural motifs across biology.
[1] Angew. Chem. Int. Ed., 2025, e202504866 doi.org/10.1002/anie.202504866; J. Am. Chem. Soc., 2023, 145, 13570. DOI: 10.1101/2023.01.04.522759; 2025 doi.org/10.1101/2025.08.21.671622; 2025, doi.org/10.1101/2025.07.06.663355
[2] Angew. Chem. Int. Ed., 2025, e202503683 doi.org/10.1002/anie.202503683
[3] Angew. Chem. Int. Ed., 2021, 60, 18144-51 doi:10.1002/anie.202104179
[4] Chem. Sci., 2021, 12, 7174-84 doi:10.1039/D1SC00933H
[5] Scientific Reports, 2018, 8, 13342 DOI:10.1038/s41598-018-31513-3