NMR Observation of Sulfhydryl Signals in SARS-CoV-2 Main Protease Aids Structural Studies

The 68-kDa homodimeric 3C-like protease of SARS-CoV-2, M^pro (3CL^pro /Nsp5), is a key antiviral drug target. NMR spectroscopy of this large system proved challenging and resonance assignments have remained incomplete. Here we present the near-complete (>97 %) backbone assignments of a C145A variant of M^pro (M^pro _C145A ) both with, and without, the N-terminal auto-cleavage substrate sequence, in its native homodimeric state. We also present SILLY (Selective Inversion of thioL and Ligand for NOESY), a simple yet effective pseudo-3D NMR experiment that utilizes NOEs to identify interactions between Cys-thiol or aliphatic protons, and their spatially proximate backbone amides in a perdeuterated protein background. High protection against hydrogen exchange is observed for 10 of the 11 thiol groups in M^pro _C145A , even those that are partially accessible to solvent. A combination of SILLY methods and high-resolution triple-resonance NMR experiments reveals site-specific interactions between M^pro , its substrate peptides, and other ligands, which present opportunities for competitive binding studies in future drug design efforts.