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 (Kd = 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 (ΔGTER = −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.