Design, Synthesis, and Biological Evaluation of 5,8-Dimethyl Shikonin Oximes as SARS-CoV-2 M^pro Inhibitors

We have designed, synthesized, and characterized a small library of shikonin derivatives and demonstrated their inhibitory activity against the main protease, M^pro, of SARS-CoV-2. One analog, 5,8-dimethyl shikonin oxime (15), exhibited the highest activity against SARS-CoV-2 M^pro with an IC₅₀ value of 12.53 ± 3.59 μM. It exhibited much less toxicity as compared with the parent compound, shikonin, in both in vitro and in vivo models. Structure-activity relationship analysis indicated that the oxime moieties on the naphthalene ring and the functional groups attached to the oxygen atom on the side chain play a pivotal role in enzymatic inhibitory activity. Molecular docking results implied that the inhibitor 15 is perfectly settled in the core of the substrate-binding pocket of M^pro by possibly interacting with three catalytic residues, His41, Cys145, and Met165. Overall, the shikonin oxime derivative 15 deserves further investigation as an antiviral agent against SARS-CoV-2.