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N⁶-(((trimethylsilyl)-methoxy)carbonyl)-l-lysine (TMSK) and N⁶-trifluoroacetyl-l-lysine (TFAK) are non-canonical amino acids, which can be installed in proteins by genetic encoding. In addition, we describe a new aminoacyl-tRNA synthetase specific for N⁶-(((trimethylsilyl)methyl)-carbamoyl)-l-lysine (TMSNK), which is chemically more stable than TMSK. Using the dimeric SARS-CoV-2 main protease (M^pro) as a model system with three different ligands, we show that the ¹H and ¹⁹F nuclei of the solvent-exposed trimethylsilyl and CF₃ groups produce intense signals in the nuclear magnetic resonance (NMR) spectrum. Their response to active-site ligands differed significantly when positioned near rather than far from the active site. Conversely, the NMR probes failed to confirm the previously reported binding site of the ligand pelitinib, which was found to enhance the activity of M^pro by promoting the formation of the …