Modulating Ribosomal Frameshifts to Interfere with Viral Protein Translation

Modulating Ribosomal Frameshifts to Interfere with Viral Protein Translation Modulating Ribosomal Frameshifts to Interfere with Viral Protein Translation The -1 programmed ribosomal frameshift (PRF) is associated with viral protein translation in cells infected with SARS-CoV, SARS-CoV-2, HIV and other viruses. The -1 PRF is caused by a slippery sequence in the mRNA and nearby secondary structures, most prominently a downstream pseudoknot. This event leads to a stochastic shift of the reading frame of a translating ribosome and controls the expression of key viral proteins (the RNA replicase, in case of SARS-CoV-2). Successful interference with the -1 PRF mechanism could lead to a potent broad-spectrum antiviral drug against multiple and currently uncurable viral diseases. We will explore strategies to interfere with the -1 PRF in a combined experimental and computational approach. We are motivated by these key arguments: A. The -1 PRF occurs with a finely tuned probability that controls the ratio of the resulting gene products. Hence, the free energy barrier difference for translation in both reading frames is marginal, which facilitates modulation. B. Either -1 PRF inhibition and promotion would interfere with the expression and stoichiometry of the gene products. C. PRF modulation via interactions with the host protein translation machinery would severely limit the ability of the virus to adapt by mutation. Our key goals for this project are: 1. Adapt an assay that would enable a high-throughput screen of peptides and oligonucleotides for their activity to modulate -1 PRF events in mammalian cells. 2. Develop a structural model of the pseudoknot involved in -1 PRF and its interactions with the ribosome. 3. Identify potential interaction sites of peptides or oligonucleotides identified from screens to impact the -1 PRF via docking and molecular simulation.