Rapid assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy

Kantsadi, Anastassia L.; Vakonakis, Ioannis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological cause of the coronavirus disease 2019, for which no effective therapeutics are available. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and constitutes a promising therapeutic target. Recently, crystallographic fragment screening uncovered a large number of molecules binding at the Mpro active site as well as at sites of potential allostery. However, no information on fragment affinity is available. Here, we describe an efficient protocol for screening chemical compounds for binding to Mpro using saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy. We characterised the relative affinity of Mpro-binding fragments using STD-NMR, revealing a ~200-fold difference in binding potential. Combined with crystallographic structures of these fragments bound to Mpro, this information can assist ongoing drug design efforts.