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(2026-04-29 22:34):
#paper doi:10.1038/s41467-026-66923-9,In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer(Nature Communications, 2026, 17:4621)该研究针对 G 蛋白偶联受体(GPCR)纳米抗体传统发现依赖免疫文库筛选、耗时费力且成功率低的技术瓶颈,开发基于“AlphaFold-Multimer(AF-M)”的计算预测筛选策略,实现 GPCR 纳米抗体的精准从头发现。研究团队首先通过分析已知纳米抗体 - GPCR 复合物结构,建立 AF-M 输出参数(如界面接触数、pLDDT 评分、界面能量)的判别模型,能有效区分结合型与非结合型纳米抗体 - GPCR 配对;随后对含 10,000 个纳米抗体的虚拟文库进行前瞻性筛选,成功鉴定出对 MRGPRX2(介导假性过敏炎症与瘙痒的关键 GPCR 靶点)具有 20-200nM 亲和力的特异性结合纳米抗体,且通过细胞实验验证其能有效抑制 MRGPRX2 介导的肥大细胞脱颗粒信号通路。该方法无需实验免疫或文库构建,大幅缩短纳米抗体开发周期,为 GPCR 等膜蛋白靶点的快速抗体工具开发及治疗性抗体设计提供了高效计算范式,尤其适用于传统方法难以靶向的 GPCR 亚型与构象态。
bioRxiv,
2025-3-8.
DOI: 10.1101/2025.03.05.640882
In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer
Abstract:
ABSTRACT<br> <br> Antibodies are central mediators of the adaptive immune response, and they are powerful research tools and therapeutics. Antibody discovery requires substantial experimental effort, such as immunization campaigns or<br> <i>in vitro</i><br> library screening. Predicting antibody-antigen binding<br> <i>a priori</i><br> remains challenging. However, recent machine learning methods raise the possibility of<br> <i>in silico</i><br> antibody discovery, bypassing or reducing initial experimental bottlenecks. Here, we report a virtual screen using AlphaFold-Multimer (AF-M) that prospectively identified nanobody binders to MRGPRX2, a G protein-coupled receptor (GPCR) and therapeutic target for the treatment of pseudoallergic inflammation and itch. Using previously reported nanobody-GPCR structures, we identified a set of AF-M outputs that effectively discriminate between interacting and non-interacting nanobody-GPCR pairs. We used these outputs to perform a prospective<br> <i>in silico</i><br> screen, identified nanobodies that bind MRGPRX2 with high affinity, and confirmed activity in signaling and functional cellular assays. Our results provide a proof of concept for fully computational antibody discovery pipelines that can circumvent laboratory experiments.<br>
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