VPS34 inhibition as a host-targeting anti-coronaviral strategy: Rational design of YBM with optimized pharmacokinetic...

Targeting host factors critical to the viral life cycle instead of direct viral enzyme inhibition represents a promising alternative strategy for developing broad-spectrum antivirals. Here, we identified VPS34, a key regulator of autophagosome-lysosome fusion and membrane trafficking, as a conserved host-dependency factor across coronaviruses. VPS34 gene knockdown significantly attenuates viral replication both in vitro and in vivo. Crucially, this antiviral effect remained potent against emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, demonstrating that VPS34 is a drug target resilient to viral evolution. Based on the scaffold structure of the VPS34 inhibitor SAR405, we developed YBM, a novel small-molecule inhibitor, via critical group substitutions and aliphatic chain introduction. YBM exhibited superior pharmacokinetic properties than SAR405, including enhanced bioavailability and prolonged plasma half-life. YBM shows significant in vivo efficacy against SARS-CoV-2 and HCoV-OC43. Crucially, its broad-spectrum potential is underscored by potent in vitro activity against multiple coronavirus genera (α and γ). This study established YBM as a host-targeting antiviral (HTA) that targets VPS34, offering protection against both extant and evolving coronaviruses. The evolutionarily conserved role of VPS34 in mediating coronavirus replication suggests that this host factor may become a priority therapeutic target for coronaviruses during future pandemics.