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Changing the Dynamics and Structures of key viral RNA structures using nano-size supramolecular drugs
Secondary Supervisor(s): Professor Teresa Carlomagna
University of Registration: University of Birmingham
BBSRC Research Themes: Understanding the Rules of Life (Microbiology, Structural Biology)
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. In particular, the functional RNA structures in structurally-conserved untranslated regions (UTRs) of many viruses are intriguing targets. These UTRs often share common structural elements that are functionally essential and so conserved as the virus evolves (drifts) 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 either initiation of replication (for example by recruiting proteins or by direct interaction with the ribosome) or regulation of the replication cycle.
We have shown that nanoscale metallo-supramolecular cylinders are unique nano-drugs that can bind within DNA and RNA cavities, with different cylinders targeting 3-way junctions, 4-way junctions or various bulges. These cylinders can bind bulge structures in the RNA of both HIV and SARS-CoV-2 viral genome and prevent their replication in cells [1-4].
In this project we will use our world-leading expertise in high-field NMR determinations of RNA structures [5] to get unique insight into the binding events, their structural effects and the effects on the dynamic behaviour of the RNA. We will combine the NMR experimental data with molecular dynamics simulations. The work will be guided by experimental gel studies, competition assays and RNA SHAPE assessment of binding on viral UTRs, to confirm structure preference, which will then interrogated in detail. Chemical synthesis and design will be used to prepare the new binding agents, which will be fully characterised using a range of analytical techniques.
The approach and understanding developed will represent a new roadmap for design of drugs to target RNA structural motifs across biology and nucleic acid nanoscience, that can allow us to probe the role of such structures in viral infection.
References
[1] Supramolecular cylinders target bulge structures in the 5’ UTR of the RNA genome of SARS-CoV-2 and inhibit viral replication. L. Melidis, H.J. Hill, N.J. Coltman, S.P. Davies, K. Winczura, T. Chauhan, J.S. Craig, A. Garai, C.A.J. Hooper, R.T. Egan, J.A. McKeating, N.J. Hodges, Z. Stamataki, P. Grzechnik, M.J. Hannon, Angew. Chem. Int. Ed., 2021, 60, 18144-51. doi: 10.1002/anie.202104179 BioRXive doi: 10.1101/2021.03.30.437757
[2] Targeting structural features of viral genomes with a nano-sized supramolecular drug. L. Melidis, I.B. Styles, M.J. Hannon, Chem. Sci., 2021, 12, 7174-84. doi: 10.1039/D1SC00933H
[3] Metallo supramolecular cylinders inhibit HIV-1 TAR-TAT complex formation and viral replication in cellulo. L. Cardo, I. Nawroth, P.J. Cail, J.A. McKeating, M. J. Hannon, Scientific Reports, 2018, 8, Article number 13342. DOI: 10.1038/s41598-018-31513-3.
[4]Organometallic Pillarplexes that bind DNA 4-way Holliday Junctions and forks. J.S. Craig, L. Melidis, H.D. Williams, S.J. Dettmer, A.A. Heidecker, P.J. Altmann, S.Guan, C. Campbell, D.F. Browning, R.K.O. Sigel, S. Johannsen, R.T. Egan, B. Aikman, A. Casini, A. Pöthig, M.J. Hannon, J. Am. Chem. Soc., 2023, 145, 13570. DOI: 10.1101/2023.01.04.522759.
[5]Solid-state NMR Spectroscopy of RNA. A Marchanka & T Carlomagno, Methods in Enzymology, 2019, 615, 333–371.