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.

基于蛋白降解靶向嵌合体（PROTACs）的靶向蛋白质降解在抗病毒治疗领域展现出巨大应用潜力，但受限于三元复合物形成效率低下的核心挑战。本研究报道了靶向新型冠状病毒（SARS-CoV-2）RNA依赖的RNA聚合酶（RdRp）的PROTACs的从头设计工作。研究团队借助再利用的抗病毒药物骨架，并对E3泛素连接酶（E3 ligase）配体进行优化，共设计并筛选了600个候选化合物。通过整合式筛选流程，我们鉴定出PROTAC 10——一种莫努匹拉韦（molnupiravir）-脑型肿瘤相关蛋白（CRBN）偶联物。该化合物在感染细胞中表现出高亲和力结合能力（解离常数Kd=1.09 nM）、显著的正协同效应（协同系数α=45.9），以及经CRBN介导的高效RdRp降解活性（降解半数有效浓度DC50=1.97 μM）。PROTAC 10通过模块化点击化学（铜催化叠氮-炔环加成，CuAAC）合成，其结构中合理引入了以柔性烷基间隔臂侧翼连接的中心三唑环。该化合物展现出强效抗病毒活性（半数抑制浓度IC50=3.12 μM）。分子动力学模拟结果显示，其工程化设计的连接臂可增强协同效应、提升三元复合物稳定性（ΔGTER=−247 kcal/mol），并赋予分子构象变色龙特性。本研究为通过合理优化连接臂以实现选择性病毒蛋白降解的抗病毒PROTACs设计，提供了一套系统性的策略框架。