Structure-Informed Design of High-Cooperativity PROTAC Targeting SARS-CoV-2 RdRp via Click Chemistry and Enhanced Sampling Simulations

Targeted protein degradation via PROTACs holds promise for antiviral therapy but is challenged by inefficient ternary complex formation. We report the de novo design of PROTACs targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Leveraging repurposed antiviral scaffolds and optimizing E3 ligase ligands, we designed and screened 600 candidates. Our integrated pipeline identified PROTAC 10, a molnupiravir-CRBN conjugate, which demonstrated high-affinity binding (<i>K</i>_d = 1.09 nM), pronounced positive cooperativity (α = 45.9), and effective CRBN-mediated RdRp degradation (DC₅₀ = 1.97 μM) in infected cells. PROTAC 10 was synthesized by using modular click chemistry (CuAAC), strategically incorporating a central triazole ring flanked by flexible alkyl spacers. It exhibited potent antiviral activity (IC₅₀ = 3.12 μM). Molecular dynamics simulations revealed that its engineered linker enhances cooperativity, ternary complex stability (Δ<i>G</i>_TER = -247 kcal/mol), and chameleonic character. This study provides a strategic framework to design antiviral PROTACs through rational linker optimization that enables selective viral protein degradation.