Targeting the SARS-CoV-2 RNA translation initiation element SL1 by molecules of low molecular weight

We present the development of low molecular weight inhibitors that target the 5’-terminal RNA stem-loop 1 (SL1) of the SARS-CoV-2 genome. SL1 is crucial for allowing viral protein synthesis in the context of global translation repression in infected cells. We applied compound- and RNA-detected nuclear magnetic resonance spectroscopy (NMR) experiments to guide a fragment-growth strategy based on two primary NMR screening hits from a diverse fragment library poised for follow-up chemistry. These primary hits with molecular weights of around 200 Da were derivatized with the aim to improve solubility, binding affinity, and target specificity. We used NMR to monitor solubility changes, binding affinity, and specific binding to the SL1 binding pocket along the fragment derivatization campaign. The six compounds scoring best in all three categories were tested for their inhibitory effect on SL1 in a cell-free translation assay, where the best two compounds, A.2 and A.13, showed both significant and selective inhibition. Our results demonstrate that small molecules targeting translation initiation of SARS-CoV-2 can be rapidly obtained using NMR-guided medicinal chemistry, and that the correlation between affinity, selectivity, and in situ function of the derived compounds is still to be explored.