The control of potato virus Y (PVY) induced crop failure is a challengeable issue in agricultural chemistry. Although many anti‐PVY agents are designed to focus on the functionally important coat protein (CP) of virus, how these drugs act on CP to inactivate viral pathogenicity, remains largely unknown. Herein, a PVY CP inhibitor ‐3j (S) is disclosed, which is accessed by developing unusually efficient (up to 99% yield) and chemo‐selective (> 99:1 er in most cases) carbene‐catalyzed [3+4] cycloaddition reactions. Compound ‐3j bears a unique arylimidazole‐fused diazepine skeleton and shows chirality‐preferred performance against PVY. In addition, ‐3j (S) as a mediator allows ARG191 (R¹⁹¹) of CP to be identified as a key amino acid site responsible for intercellular movement of virions. R¹⁹¹ is further demonstrated to be critical for the interaction between PVY CP and the plant functional protein NtCPIP, enabling virions to cross plasmodesmata. This key step can be significantly inhibited through bonding with the ‐3j (S) to further impair pathogenic behaviors involving systemic infection and particle assembly. The study reveals the in‐depth mechanism of action of antiviral agents targeting PVY CP, and contributes to new drug structures and synthetic strategies for PVY management.

In this study, a commercial agent with antivirus activity and moroxydine hydrochloride were employed to perform a lead optimization. A series of 1,3,5-triazine derivatives with piperazine structures were devised and synthesized, and an evaluation of their anti-potato virus Y (PVY) activity revealed that several of the target compounds possessed potent anti-PVY activity. The synthesis of compound C35 was directed by a 3D-quantitative structure–activity relationship that used the compound’s structural parameters. The assessment of the anti-PVY activity of compound C35 revealed that its curative, protective, and inactivation activities (53.3 ± 2.5%, 56.9 ± 1.5%, and 85.8 ± 4.4%, respectively) were comparable to the positive control of ningnanmycin (49.1 ± 2.4%, 50.7 ± 4.1%, and 82.3 ± 6.4%) and were superior to moroxydine hydrochloride (36.7 ± 2.7%, 31.4 ± 2.0%, and 57.1 ± 1.8%). In addition, molecular docking demonstrated that C35 can form hydrogen bonds with glutamic acid at position 150 (GLU 150) of PVY CP, providing a partial theoretical basis for the antiviral activity of the target compounds.