Lycorine esters exert anti-HCoV-OC43 effect through reversibly acylating cysteine residue in the nsp 12 NiRAN domain

By introducing ester warheads into the hydroxyl groups in lycorine (1), three types of lycorine mono-ester or di-ester analogues were synthesized and evaluated for their antiviral activities against HCoV-OC43. Most of them showed higher selective indexes (SI) than 1, up to nearly 14 times. Using compound 6b as a probe, we firstly demonstrated that lycorine esters directly targeted nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain in the non-structural protein 12 (nsp 12) by reversibly acylating Cys12 to induce the shrink of NiRAN pocket and block the viral replication, different from the known RdRp inhibitors. Meanwhile, the reversible acylation mode of lycorine esters guaranteed the higher SI values and long-acting effects of its kind. Thus, in addition to acting as prodrugs, ester compounds with a highly acylating warhead can be used as covalent probes to explore the detailed mode of action and improve the safety window. Compound 6b has been identified as a new reversible covalent RdRp allosteric inhibitor for further investigation.